Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1611714 original size:134 final size:133
Alignment explanation
Indices: 1611375--1611894 Score: 480
Period size: 134 Copynumber: 3.9 Consensus size: 133
1611365 ATATTGTATT
* * * * * * * *
1611375 TGCTCCACTATTTCTTCAGGGTAGATCAGA-TCG-GAATGA-TTTGATTCAATTCACTGTTCTTC
1 TGCTCCACTA-CTCTTTAGGGGAGATCAGACTCGAGAA-AATTTTGATCCACTTCGCTGCTCTTC
* * * *
1611437 CGGGGAGATTGAATCAGAACCGATTTGCTTCACTGCTCTTTAGGAAGACTAAAATCTGAAAA-AA
64 AGGGAAGATTGAATCAGAA-CAATTTGCTTCACTGCTCTTTAGGAAGAC-CAAATCT-AAAAGAA
* * *
1611501 GAATAATT
126 GGAGAATC
* * * * ** *
1611509 TTCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGGTCCTA-TTCACTATTCTTTA
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCC-ACTTCGCTGCTCTTCA
* *
1611573 GGTAAGATTGAATCAGAATCAATTTGCTCCACTGCTCTTTAGGAAGACCAAATCTAAAAGAAGGA
65 GGGAAGATTGAATCAGAA-CAATTTGCTTCACTGCTCTTTAGGAAGACCAAATCTAAAAGAAGGA
1611638 GAATC
129 GAATC
* * *
1611643 TGCTCCACTACTCTTTAGGGGAAATCAGACTTGAGAAAATTTTGATCCACTTTGCTGCTCTTCAG
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTGCTCTTCAG
* * * * * *
1611708 GGAAGATTGAATCA-AACATGATTTGCTTCACTTCTCTTCAGGAATACCAAATATGAAAGAAAGA
66 GGAAGATTGAATCAGAACA--ATTTGCTTCACTGCTCTTTAGGAAGACCAAATCTAAAAGAAGGA
1611772 GAATC
129 GAATC
* ** * * * *
1611777 TGTTCCACTACTCTTTA-AAGAGATCTGACTCGAGAAAGTTTTGATCCACTTCGCTGGTCTTCAA
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTGCTCTTCAG
* * ** *
1611841 GGAAGATTGAATCA-AACATGATTTGTTTCGCTGCTCTTCGGGAATACCAAATCT
66 GGAAGATTGAATCAGAACA--ATTTGCTTCACTGCTCTTTAGGAAGACCAAATCT
1611895 TAAACAAAAA
Statistics
Matches: 326, Mismatches: 52, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
132 2 0.01
133 110 0.34
134 150 0.46
135 63 0.19
136 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (133 bp):
TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGCTGCTCTTCAG
GGAAGATTGAATCAGAACAATTTGCTTCACTGCTCTTTAGGAAGACCAAATCTAAAAGAAGGAGA
ATC
Found at i:1612821 original size:45 final size:44
Alignment explanation
Indices: 1612687--1612857 Score: 101
Period size: 45 Copynumber: 3.8 Consensus size: 44
1612677 AATGATAACT
* * * ** * *
1612687 CCAAAAGATTGACTACTCTTCGCGAGAAAGTCAAGAAGGCAACA
1 CCAAAAGACTAACTTCTCTTCATGAGAAAGTCAAGAAGACAAAA
* * * * * * ** *
1612731 CTAAAATATTGACTCCTTTTCACAAGAACGTCAAGGAAGACAAAA
1 CCAAAAGACTAACTTCTCTTCATGAGAAAGTCAA-GAAGACAAAA
* * * * *
1612776 CCGAAATATTAAC-TCATCTTCGTGAGAAAGTCAAGAAGGATAAAA
1 CCAAAAGACTAACTTC-TCTTCATGAGAAAGTCAAGAA-GACAAAA
* *
1612821 CTAAAAGACTGACTTCTCTTCATGAGAAAGTCAAGAA
1 CCAAAAGACTAACTTCTCTTCATGAGAAAGTCAAGAA
1612858 TAAAATTGAA
Statistics
Matches: 98, Mismatches: 25, Indels: 7
0.75 0.19 0.05
Matches are distributed among these distances:
44 31 0.32
45 65 0.66
46 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (44 bp):
CCAAAAGACTAACTTCTCTTCATGAGAAAGTCAAGAAGACAAAA
Found at i:1613977 original size:38 final size:38
Alignment explanation
Indices: 1612824--1613979 Score: 806
Period size: 42 Copynumber: 28.8 Consensus size: 38
1612814 GATAAAACTA
* * * *
1612824 AAAGACTGACTTCTCTTCATGAGAAAGTCAAGAATAAAATTG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AA--C
** * *
1612866 AAAGATTGACTTCAATTCACGAGGGAGTCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
1612904 AAAGATTGACCTCTCTTTATGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* **
1612942 AAAGATTGATTTCTCTTTTCGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
1612980 ATTGAAAGATTGACTAT-TATTCATGAGGGAGTCAAGAATAAC
1 ----AAAGATTGACT-TCTCTTCACGAGGAAGTCAAGAATAAC
* *
1613022 ATTGAAAGATTGATTTCTTTTCACGAGGAAGTCAAGAATGAGAAAAC
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-----AAC
* * *
1613069 TAAAAGATTGACTTCTCTTCACGAGAAAATCAAGAATAAAATTG
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AA--C
* *
1613113 AAAGATTGACTCCTCTTCACGA-GAGAGCCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGA-AGTCAAGAATAAC
* *
1613151 AAAGATTGACATCTCTTCACAAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
1613189 ATTGAAAGATTGACTTCTTTTCATGAGAAAATCAAGAATAAAATTA
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AA--C
*
1613235 AAAGATTGA-TTCCCCTTCACGA-GAGAGTCAAGAATAAC
1 AAAGATTGACTT-CTCTTCACGAGGA-AGTCAAGAATAAC
* *
1613273 ATTGAAAGATTGACTTCTCTTCACAAGGAAGTAAAGAATAAC
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
1613315 AAAGATTGAATTCTCTTCATGATGAAGTCAATAGTAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
1613353 AAAGATTTATTTCTCCTCACGAGGAAGTCGAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
1613391 AAAGATAGATGGAC-TCATCCTCACGA-GATAGTAAAGAATAAC
1 AAAGAT---T-GACTTC-TCTTCACGAGGA-AGTCAAGAATAAC
*
1613433 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** *
1613471 AAATATCAACTTCTCTTCACGA-GAAGTTAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
1613508 TTTGAAAAATTGAC-TCATCTTCACGAAGG-AGTCAAGAATAAC
1 ----AAAGATTGACTTC-TCTTCACG-AGGAAGTCAAGAATAAC
*
1613550 ATTGAAAGATTGACTTCTCTTTCATGAGGAAGTCAAGAATAAC
1 ----AAAGATTGACTTCTC-TTCACGAGGAAGTCAAGAATAAC
* * *
1613593 AAAGATTGAATTCTCTTCACGAAGAAGTCAAGAGTAA-
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
1613630 AAAG-GTGATTTCTCTTCACGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
1613667 AAAGATATATTGACTCCTCTTCACGA-GATATTCAAGAATAAA
1 AAAG----ATTGACTTCTCTTCACGAGGA-AGTCAAGAATAAC
*
1613709 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
1613747 AAATATCGACTTCTCTTCACGAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
1613785 ATTGAAAGATTAAATTCTCTTCACGAGGGAGTCAAGAATAAC
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
1613827 AAATATTGACTTCTCTTAATGAGGAAGTTAAAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** * *
1613865 ATTGAGAGATTGAATTCTCTTTGCGAGAAAGTCAAGAATGAC
1 A---A-AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
1613907 ATTGAATGATTGACTTGTCTTTACGAGAAAGTCAAGAATAAC
1 A---AA-GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* **
1613949 AAAGATTGACTTTTCTTCATAAGGAAGTCAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAA
1613980 TAATGACATT
Statistics
Matches: 902, Mismatches: 146, Indels: 136
0.76 0.12 0.11
Matches are distributed among these distances:
36 28 0.03
37 22 0.02
38 337 0.37
39 25 0.03
40 8 0.01
41 29 0.03
42 390 0.43
43 26 0.03
44 2 0.00
45 32 0.04
47 3 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:1614013 original size:80 final size:80
Alignment explanation
Indices: 1612824--1614014 Score: 886
Period size: 80 Copynumber: 14.8 Consensus size: 80
1612814 GATAAAACTA
* * * * **
1612824 AAAGACTGACTTCTCTTCATGAGAAAGTCAAGAATAAAATTGAAAGATTGACTTCAATTCACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
** *
1612889 GGAGTCAGGAATAAC
66 AAAGTCAAGAATAAC
* * * * **
1612904 AAAGATTGACCTCTCTTTATGAGGAAGTCAAGAATAAC----AAAGATTGATTTCTCTTTTCGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
*
1612965 GAAGTCAAGAATAAC
66 AAAGTCAAGAATAAC
* * * * *
1612980 ATTGAAAGATTGACTAT-TATTCATGAGGGAGTCAAGAATAACATTGAAAGATTGATTTCTTTTC
1 ----AAAGATTGACT-TCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTC
*
1613044 ACGAGGAAGTCAAGAATGAGAAAAC
61 ACGAGAAAGTCAAGAAT-----AAC
* * * *
1613069 TAAAAGATTGACTTCTCTTCACGAGAAAATCAAGAATAAAATTGAAAGATTGACTCCTCTTCACG
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACG
* *
1613134 AGAGAGCCAAGAATAAC
64 AGAAAGTCAAGAATAAC
* * * *
1613151 AAAGATTGACATCTCTTCACAAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTTTTCATGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
* *
1613216 AAAATCAAGAATAAAATTA
66 AAAGTCAAGAAT--AA--C
* *
1613235 AAAGATTGA-TTCCCCTTCACGA-GAGAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACA
1 AAAGATTGACTT-CTCTTCACGAGGA-AGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACG
* *
1613298 AGGAAGTAAAGAATAAC
64 AGAAAGTCAAGAATAAC
* * * * * * * *
1613315 AAAGATTGAATTCTCTTCATGATGAAGTCAATAGTAA-A---AAAGATTTATTTCTCCTCACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
* *
1613376 GAAGTCGAGAATAAC
66 AAAGTCAAGAATAAC
* *
1613391 AAAGATAGATGGAC-TCATCCTCACGA-GATAGTAAAGAATAAC----AAAGATTGACTTCTCTT
1 AAAGAT---T-GACTTC-TCTTCACGAGGA-AGTCAAGAATAACATTGAAAGATTGACTTCTCTT
* *
1613450 CACAAGGAAGTCAAGAATAAC
60 CACGAGAAAGTCAAGAATAAC
* ** * * *
1613471 AAATATCAACTTCTCTTCACGA-GAAGTTAAGAATAACTTTGAAAAATTGAC-TCATCTTCACGA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTC-TCTTCACGA
*
1613534 -AGGAGTCAAGAATAAC
65 GA-AAGTCAAGAATAAC
* *
1613550 ATTGAAAGATTGACTTCTCTTTCATGAGGAAGTCAAGAATAAC----AAAGATTGAATTCTCTTC
1 ----AAAGATTGACTTCTC-TTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTC
*
1613611 ACGA-AGAAGTCAAGAGTAA-
61 ACGAGA-AAGTCAAGAATAAC
* * * ** * * *
1613630 AAAG-GTGATTTCTCTTCACGAGGAAGTCAAGAATAAAAAAGATATATTGACTCCTCTTCACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
* * *
1613694 ATATTCAAGAATAAA
66 AAAGTCAAGAATAAC
* *
1613709 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA-A---AAATATCGACTTCTCTTCACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
1613770 AAAGTCAAGAATAAC
66 AAAGTCAAGAATAAC
* * * * *
1613785 ATTGAAAGATTAAATTCTCTTCACGAGGGAGTCAAGAATAAC----AAATATTGACTTCTCTTAA
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCA
* * * *
1613846 TGAGGAAGTTAAAAATAAC
62 CGAGAAAGTCAAGAATAAC
* ** * * * * *
1613865 ATTGAGAGATTGAATTCTCTTTGCGAGAAAGTCAAGAATGACATTGAATGATTGACTTGTCTTTA
1 A---A-AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCA
1613930 CGAGAAAGTCAAGAATAAC
62 CGAGAAAGTCAAGAATAAC
* ** * * * *
1613949 AAAGATTGACTTTTCTTCATAAGGAAGTCAATAATGACATTGAAAGGTTGACTCCTCTTCACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
1614014 A
66 A
1614015 GAGTAAATTT
Statistics
Matches: 899, Mismatches: 148, Indels: 128
0.77 0.13 0.11
Matches are distributed among these distances:
74 21 0.02
75 20 0.02
76 118 0.13
77 2 0.00
78 30 0.03
79 43 0.05
80 391 0.43
81 36 0.04
82 9 0.01
83 15 0.02
84 132 0.15
85 14 0.02
86 1 0.00
87 64 0.07
89 3 0.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (80 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCACGAG
AAAGTCAAGAATAAC
Found at i:1615964 original size:9 final size:8
Alignment explanation
Indices: 1615952--1616141 Score: 62
Period size: 8 Copynumber: 23.1 Consensus size: 8
1615942 ACTTGATTTA
1615952 TTTTATCTC
1 TTTT-TCTC
*
1615961 TTTTTTTC
1 TTTTTCTC
1615969 TTTTT-TC
1 TTTTTCTC
* *
1615976 TCTTTGTC
1 TTTTTCTC
1615984 TTTTTCTC
1 TTTTTCTC
1615992 TTATTTCT-
1 TT-TTTCTC
1616000 TTTTT-T-
1 TTTTTCTC
*
1616006 TTTCTTCTTT
1 TTT-TTC-TC
1616016 TTTTTCTC
1 TTTTTCTC
*
1616024 TTATTTCTT
1 TT-TTTCTC
1616033 TTTTTCTTC
1 TTTTTC-TC
1616042 TTTCTT-TCC
1 TTT-TTCT-C
1616051 TCTTTTCTC
1 T-TTTTCTC
* *
1616060 -TTTGCTA
1 TTTTTCTC
1616067 TTTTT-TCC
1 TTTTTCT-C
1616075 TTTTTCT-
1 TTTTTCTC
*
1616082 TTTTATATC
1 TTTT-TCTC
1616091 -TTTTCT-
1 TTTTTCTC
1616097 TTTTTCCTTC
1 TTTTT-C-TC
*
1616107 TTTTTTTC
1 TTTTTCTC
1616115 TATATTT-TC
1 T-T-TTTCTC
1616124 TCTTTTCT-
1 T-TTTTCTC
1616132 TTTTATCTC
1 TTTT-TCTC
1616141 T
1 T
1616142 ATATTTTTTA
Statistics
Matches: 140, Mismatches: 15, Indels: 52
0.68 0.07 0.25
Matches are distributed among these distances:
6 4 0.03
7 30 0.21
8 52 0.37
9 38 0.27
10 16 0.11
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTTTCTC
Found at i:1615974 original size:7 final size:7
Alignment explanation
Indices: 1615962--1616135 Score: 93
Period size: 7 Copynumber: 23.7 Consensus size: 7
1615952 TTTTATCTCT
1615962 TTTTTTC
1 TTTTTTC
1615969 TTTTTTC
1 TTTTTTC
*
1615976 TCTTTGTC
1 T-TTTTTC
1615984 TTTTTCTC
1 TTTTT-TC
*
1615992 TTATTTC
1 TTTTTTC
1615999 TTTTTT-
1 TTTTTTC
1616005 TTTTCTTC
1 TTTT-TTC
1616013 TTTTTTTTC
1 --TTTTTTC
1616022 TCTTATTTC
1 T-TT-TTTC
1616031 TTTTTTTC
1 -TTTTTTC
*
1616039 TTCTTTC
1 TTTTTTC
**
1616046 TTTCCTC
1 TTTTTTC
*
1616053 TTTTCTC
1 TTTTTTC
** *
1616060 TTTGCTA
1 TTTTTTC
1616067 TTTTTTC
1 TTTTTTC
*
1616074 CTTTTTC
1 TTTTTTC
*
1616081 TTTTTATA
1 TTTTT-TC
*
1616089 TCTTTTC
1 TTTTTTC
1616096 TTTTTTC
1 TTTTTTC
* *
1616103 -CTTCT-
1 TTTTTTC
1616108 TTTTTTC
1 TTTTTTC
1616115 TATATTTTC
1 T-T-TTTTC
*
1616124 TCTTTTC
1 TTTTTTC
1616131 TTTTT
1 TTTTT
1616136 ATCTCTATAT
Statistics
Matches: 127, Mismatches: 26, Indels: 28
0.70 0.14 0.15
Matches are distributed among these distances:
6 10 0.08
7 73 0.57
8 24 0.19
9 15 0.12
10 5 0.04
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (7 bp):
TTTTTTC
Found at i:1615987 original size:15 final size:15
Alignment explanation
Indices: 1615963--1616141 Score: 100
Period size: 15 Copynumber: 11.1 Consensus size: 15
1615953 TTTATCTCTT
1615963 TTTTTCTTTTTTCTC
1 TTTTTCTTTTTTCTC
*
1615978 TTTGTC-TTTTTCTC
1 TTTTTCTTTTTTCTC
1615992 TTATTTCTTTTTT-T-
1 TT-TTTCTTTTTTCTC
1616006 TTTCTTCTTTTTTTTCTC
1 TTT-TTC--TTTTTTCTC
1616024 TTATTTCTTTTTTTCTTC
1 TT-TTTC-TTTTTTC-TC
*
1616042 TTTCTTTCCTCTTTTCTC
1 -TT-TTT-CTTTTTTCTC
* *
1616060 TTTGCTATTTTTTC-C
1 TTT-TTCTTTTTTCTC
*
1616075 TTTTTCTTTTTATATC
1 TTTTTCTTTTT-TCTC
1616091 -TTTTCTTTTTTCCTTC
1 TTTTTCTTTTTT-C-TC
1616107 TTTTTTTCTATATTTTCTC
1 --TTTTTCT-T-TTTTCTC
1616126 -TTTTCTTTTTATCTC
1 TTTTTCTTTTT-TCTC
1616141 T
1 T
1616142 ATATTTTTTA
Statistics
Matches: 130, Mismatches: 11, Indels: 45
0.70 0.06 0.24
Matches are distributed among these distances:
13 1 0.01
14 25 0.19
15 29 0.22
16 27 0.21
17 12 0.09
18 9 0.07
19 20 0.15
20 3 0.02
21 4 0.03
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.75
Consensus pattern (15 bp):
TTTTTCTTTTTTCTC
Found at i:1616014 original size:29 final size:29
Alignment explanation
Indices: 1615965--1616135 Score: 100
Period size: 32 Copynumber: 5.5 Consensus size: 29
1615955 TATCTCTTTT
*
1615965 TTTCTTTTTTCTCTTT-GTCTTTTTCTCTTA
1 TTTCTTTTTT-T-TTTCTTCTTTTTCTCTTA
1615995 TTTCTTTTTTTTTTCTTCTTTTTTTTCTCTTA
1 TTTCTTTTTTTTTTCTTC---TTTTTCTCTTA
* *
1616027 TTTCTTTTTTTCTTCTT-TCTTTCCTCTT-
1 TTTCTTTTTTTTTTCTTCT-TTTTCTCTTA
*
1616055 TTCTCTTTGCTATTTTTTC--CTTTTTCTTTTTA
1 TT-TCTTT--T-TTTTTTCTTCTTTTTC-TCTTA
* *
1616087 TATCTTTTCTTTTTTCCTTCTTTTTTTCTATA
1 TTTCTTTT-TTTTTT-CTTCTTTTTCTCT-TA
1616119 TTTTCTCTTTTCTTTTT
1 -TTTCT-TTTT-TTTTT
1616136 ATCTCTATAT
Statistics
Matches: 111, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
28 6 0.05
29 23 0.21
30 15 0.14
31 12 0.11
32 42 0.38
33 5 0.05
34 8 0.07
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.75
Consensus pattern (29 bp):
TTTCTTTTTTTTTTCTTCTTTTTCTCTTA
Found at i:1616039 original size:40 final size:42
Alignment explanation
Indices: 1615959--1616071 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 42
1615949 TTATTTTATC
*
1615959 TCTTTTTTTCTT-TTTTCTCTTTGTCTTTTTCTCTTATTTCT
1 TCTTTTTTTCTTCTTTTCTCTTTCTCTTTTTCTCTTATTTCT
* *
1616000 TTTTTTTTTCTTCTTTT-T-TTTCTCTTATTTCT-TTTTTTCT
1 TCTTTTTTTCTTCTTTTCTCTTTCTCTT-TTTCTCTTATTTCT
* * *
1616040 TCTTTCTTTCCTCTTTTCTCTTTGCTATTTTT
1 TCTTTTTTTCTTCTTTTCTCTTT-CTCTTTTT
1616072 TCCTTTTTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 28 0.47
41 18 0.30
42 10 0.17
43 4 0.07
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (42 bp):
TCTTTTTTTCTTCTTTTCTCTTTCTCTTTTTCTCTTATTTCT
Found at i:1616094 original size:22 final size:23
Alignment explanation
Indices: 1616046--1616102 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1616036 TTCTTCTTTC
* *
1616046 TTTCCTCTTTTCTCTTTGCTATTT
1 TTTCCT-TTTTCTCTTTGATATCT
*
1616070 TTTCCTTTTTCT-TTTTATATCT
1 TTTCCTTTTTCTCTTTGATATCT
*
1616092 TTTCTTTTTTC
1 TTTCCTTTTTC
1616103 CTTCTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 17 0.59
23 6 0.21
24 6 0.21
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTCCTTTTTCTCTTTGATATCT
Found at i:1616150 original size:28 final size:27
Alignment explanation
Indices: 1615997--1616150 Score: 75
Period size: 26 Copynumber: 6.0 Consensus size: 27
1615987 TTCTCTTATT
* *
1615997 TCTTTTTTTTTTCTTCT-T-TTTTTTC
1 TCTTTTCTTTTTATTCTATATTTTTTC
*
1616022 TCTTATTTCTTTTT-TTCT-TCTTTCTTTCC
1 TC-T-TTTCTTTTTATTCTATATTT-TTT-C
* * *
1616051 TCTTTTC-TCTT-TGCTAT-TTTTTCC
1 TCTTTTCTTTTTATTCTATATTTTTTC
*
1616075 T-TTTTCTTTTTATATCT-T-TTCTTTTT
1 TCTTTTCTTTTTAT-TCTATATT-TTTTC
*
1616101 TC-CTTCTTTTT-TTCTATA--TTTTC
1 TCTTTTCTTTTTATTCTATATTTTTTC
1616124 TCTTTTCTTTTTATCTCTATATTTTTT
1 TCTTTTCTTTTTAT-TCTATATTTTTT
1616151 ATGAACTTAT
Statistics
Matches: 100, Mismatches: 11, Indels: 33
0.69 0.08 0.23
Matches are distributed among these distances:
23 11 0.11
24 16 0.16
25 11 0.11
26 35 0.35
27 16 0.16
28 8 0.08
29 3 0.03
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.75
Consensus pattern (27 bp):
TCTTTTCTTTTTATTCTATATTTTTTC
Found at i:1616150 original size:50 final size:49
Alignment explanation
Indices: 1615959--1616150 Score: 152
Period size: 50 Copynumber: 3.9 Consensus size: 49
1615949 TTATTTTATC
*
1615959 TCTTTTTTTC--TTTTTTCTCTTTGTC-TTTTTCTCTTATTTCTTTT--T
1 TCTTTTTTTCTATTTTTTCTCTTTTTCTTTTTTCTCTTATTT-TTTTCCT
* * * *
1616004 T-TTTTCTTCTTTTTTTTCTCTTATTTCTTTTTT-TCTTCTTTCTTTCC-
1 TCTTTTTTTCTATTTTTTCTCTT-TTTCTTTTTTCTCTTATTTTTTTCCT
* *
1616051 TCTTTTCTCTTTGCTATTTTTTC-CTTTTTCTTTTTATATCTTTTCTTTTTTCCT
1 TC-TTT-T-TTT-CTATTTTTTCTCTTTTTCTTTTT-TCTCTTAT-TTTTTTCCT
*
1616105 TCTTTTTTTCTATATTTTCTC-TTTTCTTTTTATCTCTATATTTTTT
1 TCTTTTTTTCTATTTTTTCTCTTTTTCTTTTT-TCTCT-TATTTTTT
1616151 ATGAACTTAT
Statistics
Matches: 119, Mismatches: 11, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
44 7 0.06
45 1 0.01
46 14 0.12
47 11 0.09
48 5 0.04
49 3 0.03
50 39 0.33
51 12 0.10
52 15 0.13
53 10 0.08
54 2 0.02
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (49 bp):
TCTTTTTTTCTATTTTTTCTCTTTTTCTTTTTTCTCTTATTTTTTTCCT
Found at i:1616150 original size:65 final size:65
Alignment explanation
Indices: 1616027--1616152 Score: 148
Period size: 65 Copynumber: 1.9 Consensus size: 65
1616017 TTTTCTCTTA
* * * * * *
1616027 TTTCTTTTTTTCTTCTTTCTTTCCTCTTTTCTCTTTGCTATTTTTTCCTTTTTCTTTTTATATCT
1 TTTCTTTTTTCCTTCTTTCTTTCATATTTTCTCTTTGCTATTTTATCCTATATCTTTTTATATCT
* *
1616092 TTTCTTTTTTCCTTCTTTTTTTCTATATTTTCTCTTTTCT-TTTTATCTCTATAT-TTTTTAT
1 TTTCTTTTTTCCTTCTTTCTTTC-ATATTTTCTCTTTGCTATTTTATC-CTATATCTTTTTAT
1616153 GAACTTATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 34 0.67
66 17 0.33
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (65 bp):
TTTCTTTTTTCCTTCTTTCTTTCATATTTTCTCTTTGCTATTTTATCCTATATCTTTTTATATCT
Found at i:1625785 original size:3 final size:3
Alignment explanation
Indices: 1625769--1625820 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
1625759 TCCTGCAAAG
* * * *
1625769 ATA ATA A-A AAA ATA ATA ATA ATA ATA ATA ATA ATG ACA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1625816 ATA AT
1 ATA AT
1625821 TAGTTTCGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1643942 original size:21 final size:20
Alignment explanation
Indices: 1643917--1643955 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1643907 AATCAAAGTC
*
1643917 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
1643938 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
1643956 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:1649777 original size:2 final size:2
Alignment explanation
Indices: 1649770--1649803 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1649760 ATATAAATTA
*
1649770 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1649804 TAAGGTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1655015 original size:13 final size:13
Alignment explanation
Indices: 1654997--1655021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1654987 TGTGCATAAG
1654997 GCAAGTCTTTATT
1 GCAAGTCTTTATT
1655010 GCAAGTCTTTAT
1 GCAAGTCTTTAT
1655022 GGTATATGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
GCAAGTCTTTATT
Found at i:1661612 original size:4 final size:4
Alignment explanation
Indices: 1661603--1661653 Score: 50
Period size: 4 Copynumber: 12.0 Consensus size: 4
1661593 TTTAAAAAAT
*
1661603 TAAA TAAA TAAA TAAA AATAA TAAA T-AA TAATA TAAA TAATA TATAA
1 TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAA-A TAAA TAA-A TA-AA
1661650 TAAA
1 TAAA
1661654 AACTATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 3 0.08
4 23 0.57
5 13 0.32
6 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:1661621 original size:19 final size:18
Alignment explanation
Indices: 1661597--1661655 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
1661587 ACCTGTTTTA
1661597 AAAAATTAAATAAATAAAT
1 AAAAA-TAAATAAATAAAT
1661616 AAAAAT-AATAAAT-AAT
1 AAAAATAAATAAATAAAT
*
1661632 -AATATAAATAATATATAAT
1 AAAAATAAATAA-ATA-AAT
1661651 AAAAA
1 AAAAA
1661656 CTATATAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.12
16 8 0.24
17 9 0.27
18 1 0.03
19 8 0.24
20 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATAAATAAATAAAT
Found at i:1661625 original size:13 final size:13
Alignment explanation
Indices: 1661604--1661653 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1661594 TTAAAAAATT
1661604 AAATAAATAAATAA
1 AAAT-AATAAATAA
1661618 AAATAATAAATAA
1 AAATAATAAATAA
*
1661631 TAAT-ATAAATAA
1 AAATAATAAATAA
*
1661643 TATATAATAAA
1 -AAATAATAAA
1661654 AACTATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:1661663 original size:25 final size:25
Alignment explanation
Indices: 1661605--1661653 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1661595 TAAAAAATTA
1661605 AATAA-ATAAATAAAAATAATAAAT
1 AATAATATAAATAAAAATAATAAAT
*
1661629 AATAATATAAATAATATATAATAAA
1 AATAATATAAATAA-AAATAATAAA
1661654 AACTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 8 0.36
26 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
AATAATATAAATAAAAATAATAAAT
Found at i:1661689 original size:18 final size:17
Alignment explanation
Indices: 1661666--1661704 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
1661656 CTATATAACA
1661666 TATATTATTTTCAAAAAT
1 TATATT-TTTTCAAAAAT
1661684 TATA-TTTTTCAAAAAT
1 TATATTTTTTCAAAAAT
1661700 TATAT
1 TATAT
1661705 ATTATATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 15 0.75
17 1 0.05
18 4 0.20
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATTTTTTCAAAAAT
Found at i:1661707 original size:18 final size:16
Alignment explanation
Indices: 1661673--1661704 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1661663 ACATATATTA
1661673 TTTTCAAAAATTATAT
1 TTTTCAAAAATTATAT
1661689 TTTTCAAAAATTATAT
1 TTTTCAAAAATTATAT
1661705 ATTATATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTCAAAAATTATAT
Found at i:1661780 original size:23 final size:20
Alignment explanation
Indices: 1661726--1661780 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
1661716 TTCCAAAAAT
1661726 CGTTTTAAAAAACTATATATA
1 CGTTTT-AAAAACTATATATA
* *
1661747 TGTTTTCAAAACTATATTATTTA
1 CGTTTTAAAAACTATA-TA--TA
1661770 CGTTTTAAAAA
1 CGTTTTAAAAA
1661781 ATTGTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
23 11 0.41
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (20 bp):
CGTTTTAAAAACTATATATA
Found at i:1661850 original size:37 final size:37
Alignment explanation
Indices: 1661749--1661989 Score: 158
Period size: 37 Copynumber: 6.5 Consensus size: 37
1661739 TATATATATG
* * * * *
1661749 TTTTCAAAACTATATTATTTACGTTTTAAAAAATTGT-
1 TTTTCAAAACTATATAATATATGTTTTCAAAAA-CGTA
* *
1661786 TTTT-AAAACTATATATATTATACGTTTTCAAAAATGTA
1 TTTTCAAAACTATATA-A-TATATGTTTTCAAAAACGTA
* *
1661824 TTTTCAAAACTATATAATATATGTTTTCAAAAACATG
1 TTTTCAAAACTATATAATATATGTTTTCAAAAACGTA
* *
1661861 TTTTCAAAACCATAGT-ATGTA--TTTTCAAAAACCG-A
1 TTTTCAAAACTATA-TAATATATGTTTTCAAAAA-CGTA
* * *
1661896 TTTTTAAAAAACTATATATTATATGCTTTCAAAAA---A
1 -TTTT-CAAAACTATATAATATATGTTTTCAAAAACGTA
* * * * **
1661932 ATATGAAAACTATATATTATATGTTTTCAAAAAAATA
1 TTTTCAAAACTATATAATATATGTTTTCAAAAACGTA
*
1661969 TTTTCAAAAACTATATTATAT
1 TTTTC-AAAACTATATAATAT
1661990 TATTATATAT
Statistics
Matches: 164, Mismatches: 25, Indels: 29
0.75 0.11 0.13
Matches are distributed among these distances:
34 27 0.16
35 12 0.07
36 17 0.10
37 55 0.34
38 33 0.20
39 20 0.12
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.42
Consensus pattern (37 bp):
TTTTCAAAACTATATAATATATGTTTTCAAAAACGTA
Found at i:1661941 original size:34 final size:34
Alignment explanation
Indices: 1661903--1661969 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1661893 CGATTTTTAA
1661903 AAAACTATATATTATATGCTTTCAAAAAAATATG
1 AAAACTATATATTATATGCTTTCAAAAAAATATG
*
1661937 AAAACTATATATTATATGTTTTCAAAAAAATAT
1 AAAACTATATATTATATGCTTTCAAAAAAATAT
1661970 TTTCAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAACTATATATTATATGCTTTCAAAAAAATATG
Found at i:1664974 original size:81 final size:81
Alignment explanation
Indices: 1664838--1665580 Score: 1136
Period size: 81 Copynumber: 9.2 Consensus size: 81
1664828 ACAATTTTAA
** * * *
1664838 CCATTATTCTTTTACTCAAAAGTATCTAACCGTTCATCTAACTGGCATAATTGGTACCTTCCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
*
1664903 CAATTGCATAGTTAGG
66 CAATTGCACAGTTAGG
* * * *
1664919 CCATTATTCTGTTACTCAACGGTATTTAACCGTTCATCTAACTGGTATAACTGGTACATTTATA-
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
*
1664983 CAATTGCACAGTTAGA
66 CAATTGCACAGTTAGG
* * * *
1664999 CCATTATTCTTTTACTCAACGATATTTAATCGTTCATCTAACTGGCATAATTAGTACTTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
* *
1665064 TAATTGCACAGTTAGT
66 CAATTGCACAGTTAGG
* * *
1665080 CCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAATTGTCATAATTGGTATC-TTTCTA
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTA-CATTTCTA
1665144 CCAATTGCACAGTTAGG
65 CCAATTGCACAGTTAGG
*
1665161 CCATTATTCTTTTACTCAACGTTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
*
1665226 CAATTGCACAATTAGG
66 CAATTGCACAGTTAGG
1665242 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1665307 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
** * * * *
1665323 -CATTA-T-TTTTACTCAACGGTATTTAATTGTTCATTTAACTAGCATAATCGATACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1665385 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
* * ** * *
1665401 CTATTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGATATAATTTGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1665466 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
1665482 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1665547 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
1665563 CCATTATTCTTTTACTCA
1 CCATTATTCTTTTACTCA
1665581 TCCATCTAAC
Statistics
Matches: 598, Mismatches: 58, Indels: 12
0.90 0.09 0.02
Matches are distributed among these distances:
78 66 0.11
79 5 0.01
80 77 0.13
81 449 0.75
82 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
CAATTGCACAGTTAGG
Found at i:1665500 original size:321 final size:322
Alignment explanation
Indices: 1664838--1665580 Score: 1172
Period size: 321 Copynumber: 2.3 Consensus size: 322
1664828 ACAATTTTAA
* * * *
1664838 CCATTATTCTTTTACTCAAAAGTATCTAACCGTTCATCTAACTGGCATAATTGGTACCTTCCTAC
1 CCATTATTCTTTTACTC-AACGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
* * *
1664903 CAATTGCATAGTTAGGCCATTATTCTGTTACTCAACGGTATTTAACCGTTCATCTAACTGGTATA
65 CAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATA
1664968 ACTGGTACATTTATACAATTGCACAGTTAGACCATTATTCTTTTACTCAACGATATTTAATCGTT
130 ACTGGTACATTTATACAATTGCACAGTTAGACCATTATTCTTTTACTCAACGATATTTAATCGTT
* * * * *
1665033 CATCTAACTGGCATAATTAGTACTTTTCTACTAATTGCACAGTTAGTCCATTATTCTTTTACTCA
195 CATCTAACTAGCATAATGAGTACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCA
* *
1665098 ACGGTATTTAACCATTCATCTAATTGTCATAATTGGTATCTTTCTACCAATTGCACAGTTAGG
260 ACGGTATTTAACCATTCATCTAACTGTCATAATTGGTACCTTTCTACCAATTGCACAGTTAGG
1665161 CCATTATTCTTTTACTCAACGTTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAACG-TATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
*
1665226 CAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATA
65 CAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATA
* * * * *
1665291 ATTGGTACATTTCTACCAATTGCACAGTTAG-GCATTA-T-TTTTACTCAACGGTATTTAATTGT
130 ACTGGTACATTTATA-CAATTGCACAGTTAGACCATTATTCTTTTACTCAACGATATTTAATCGT
* *
1665353 TCATTTAACTAGCATAATCGA-TACATTTCTACCAATTGCACAGTTAGGCTATTATTCTTTTACT
194 TCATCTAACTAGCATAAT-GAGTACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACT
** *
1665417 CAACGGTATTTAACTGTTCATCTAACTGAT-ATAATTTGTACCTTTCTACCAATTGCACAGTTAG
258 CAACGGTATTTAACCATTCATCTAACTG-TCATAATTGGTACCTTTCTACCAATTGCACAGTTAG
1665481 G
322 G
1665482 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAAC-GTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1665547 CAATTGCACAGTTAGGCCATTATTCTTTTACTCA
65 CAATTGCACAGTTAGGCCATTATTCTTTTACTCA
1665581 TCCATCTAAC
Statistics
Matches: 389, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
321 231 0.59
322 7 0.02
323 136 0.35
324 15 0.04
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (322 bp):
CCATTATTCTTTTACTCAACGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTACC
AATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAA
CTGGTACATTTATACAATTGCACAGTTAGACCATTATTCTTTTACTCAACGATATTTAATCGTTC
ATCTAACTAGCATAATGAGTACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
CGGTATTTAACCATTCATCTAACTGTCATAATTGGTACCTTTCTACCAATTGCACAGTTAGG
Found at i:1666231 original size:20 final size:20
Alignment explanation
Indices: 1666206--1666278 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 20
1666196 CGATGTTGTC
1666206 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
*
1666226 TGGTATCGATACTACCCTT-CTA
1 TGGTATCG--A-TACCCTTACCA
* *
1666248 TGGTACCGATACCCCTA-C-
1 TGGTATCGATACCCTTACCA
1666266 TGGTATCGATACC
1 TGGTATCGATACC
1666279 AAAATTAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.27
19 6 0.14
20 9 0.20
22 10 0.23
23 7 0.16
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.30
Consensus pattern (20 bp):
TGGTATCGATACCCTTACCA
Found at i:1666257 original size:22 final size:23
Alignment explanation
Indices: 1666215--1666259 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1666205 CTGGTATCGA
*
1666215 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTACCGATAC
*
1666238 TACCCTT-CTATGGTACCGATAC
1 TACCCTTACCATGGTACCGATAC
1666260 CCCTACTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (23 bp):
TACCCTTACCATGGTACCGATAC
Found at i:1666275 original size:94 final size:94
Alignment explanation
Indices: 1666151--1666335 Score: 266
Period size: 94 Copynumber: 2.0 Consensus size: 94
1666141 TACTTCTATA
* * *
1666151 CTATAGTACCGATATCCCTTCGGGTATCGATACCAAAACTAGGTTCGATGTTGTC-TGGTATCGA
1 CTATAGTACCGATACCCCTACGGGTATCGATACCAAAACTAGATT-GATGTT-TCTTGGTATCGA
1666215 TA-CCCTTACCATGGTATCGATACTACCCTT
64 TACCCCTTACCATGGTATCGATACTACCCTT
* * *
1666245 CTATGGTACCGATACCCCTACTGGTATCGATACCAAAATTAGATTGATGTTTCTTGGTATCGATA
1 CTATAGTACCGATACCCCTACGGGTATCGATACCAAAACTAGATTGATGTTTCTTGGTATCGATA
* *
1666310 CCCCTTATCATGGTATTGATACTACC
66 CCCCTTACCATGGTATCGATACTACC
1666336 TCATCTGTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
92 2 0.02
93 17 0.21
94 62 0.77
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (94 bp):
CTATAGTACCGATACCCCTACGGGTATCGATACCAAAACTAGATTGATGTTTCTTGGTATCGATA
CCCCTTACCATGGTATCGATACTACCCTT
Found at i:1678542 original size:12 final size:13
Alignment explanation
Indices: 1678519--1678569 Score: 72
Period size: 12 Copynumber: 4.1 Consensus size: 13
1678509 TGTTTGAAAG
1678519 ATAATAAT-ATAA
1 ATAATAATAATAA
1678531 ATAA-AATAATAA
1 ATAATAATAATAA
1678543 ATAATAAT-ATAA
1 ATAATAATAATAA
1678555 ATAATATATAATAA
1 ATAATA-ATAATAA
1678569 A
1 A
1678570 AACTATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.09
12 22 0.63
13 5 0.14
14 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:1678550 original size:24 final size:26
Alignment explanation
Indices: 1678519--1678569 Score: 88
Period size: 24 Copynumber: 2.0 Consensus size: 26
1678509 TGTTTGAAAG
1678519 ATAATAATATAAATAA-A-ATAATAA
1 ATAATAATATAAATAATATATAATAA
1678543 ATAATAATATAAATAATATATAATAA
1 ATAATAATATAAATAATATATAATAA
1678569 A
1 A
1678570 AACTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 16 0.64
25 1 0.04
26 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
ATAATAATATAAATAATATATAATAA
Found at i:1678556 original size:19 final size:18
Alignment explanation
Indices: 1678530--1678568 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1678520 TAATAATATA
1678530 AATAAAATAATAAATAAT
1 AATAAAATAATAAATAAT
*
1678548 AATATAAATAATATATAAT
1 AATA-AAATAATAAATAAT
1678567 AA
1 AA
1678569 AAACTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAATAATAAATAAT
Found at i:1678649 original size:38 final size:35
Alignment explanation
Indices: 1678605--1678920 Score: 225
Period size: 36 Copynumber: 8.7 Consensus size: 35
1678595 CAAAAATAAT
* *
1678605 ATGTTTTCAAAAATTATTATTATATATGTTTCCAAAA
1 ATGTTTTC-AAAACTA-TATTATATATGTTTTCAAAA
* *
1678642 ATCGTTTTGAAAA--ACTA-TATATATGTTTTCAAATT
1 AT-GTTTTCAAAACTA-TATTATATATGTTTTCAAA-A
*
1678677 ATGTTTTCAAAACTATATTATATACGTTTTCAAAA
1 ATGTTTTCAAAACTATATTATATATGTTTTCAAAA
* * *
1678712 ATAGTTTTTAAAATTATATATATTATACGTTTTCAAAA
1 AT-GTTTTCAAAACTATAT-TA-TATATGTTTTCAAAA
*
1678750 ATGTGTTTTCAAAACTATATAATATATGTTTTCGAAAA
1 A--TGTTTTCAAAACTATATTATATATGTTTTC-AAAA
* *
1678788 CGTGTTTTCAAAACCATATTATATA--TTTTCAAAA
1 -ATGTTTTCAAAACTATATTATATATGTTTTCAAAA
* * *
1678822 ACTAATTTTTAAAAACTATA-TATTATATGCTTTCAAAAA
1 A-T--GTTTTCAAAACTATATTA-TATATGTTTTC-AAAA
* *
1678861 ACGTTTTCTAAAAACTATA-TAGCATATGTTTTCAAAA
1 ATGTTTTC--AAAACTATATTA-TATATGTTTTCAAAA
**
1678898 A-AATTTCAAAAACTATATTATAT
1 ATGTTTTC-AAAACTATATTATAT
1678921 TATTATATAT
Statistics
Matches: 227, Mismatches: 30, Indels: 46
0.75 0.10 0.15
Matches are distributed among these distances:
34 29 0.13
35 28 0.12
36 56 0.25
37 44 0.19
38 50 0.22
39 19 0.08
40 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (35 bp):
ATGTTTTCAAAACTATATTATATATGTTTTCAAAA
Found at i:1678681 original size:13 final size:13
Alignment explanation
Indices: 1678663--1678687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1678653 AAACTATATA
1678663 TATGTTTTCAAAT
1 TATGTTTTCAAAT
1678676 TATGTTTTCAAA
1 TATGTTTTCAAA
1678688 ACTATATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TATGTTTTCAAAT
Found at i:1678781 original size:37 final size:37
Alignment explanation
Indices: 1678606--1678898 Score: 212
Period size: 38 Copynumber: 7.9 Consensus size: 37
1678596 AAAAATAATA
* * *
1678606 TGTTTTCAAAAATTATTATTATATATGTTTCCAAAAAT-
1 TGTTTTC-AAAACTA-TATAATATATGTTTTCAAAAATG
* * * *
1678644 CGTTTTGAAAA--ACTAT-ATATATGTTTTC-AAATTA
1 TGTTTTCAAAACTA-TATAATATATGTTTTCAAAAATG
* *
1678678 TGTTTTCAAAACTATATTATATACGTTTTCAAAAATAG
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAAT-G
* *
1678716 T-TTTT-AAAATTATATATATTATACGTTTTCAAAAATG
1 TGTTTTCAAAACTATATA-A-TATATGTTTTCAAAAATG
* *
1678753 TGTTTTCAAAACTATATAATATATGTTTTCGAAAACG
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAATG
* * *
1678790 TGTTTTCAAAACCATAT--TATATATTTTCAAAAACTAA
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAA-T-G
* * * *
1678827 T-TTTTAAAAACTATATATTATATGCTTTCAAAAAACG
1 TGTTTTCAAAACTATATAATATATGTTTTC-AAAAATG
* **
1678864 T-TTTCTAAAAACTATATAGCATATGTTTTCAAAAA
1 TGTTT-TCAAAACTATATAATATATGTTTTCAAAAA
1678899 AATTTCAAAA
Statistics
Matches: 209, Mismatches: 30, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
33 4 0.02
34 20 0.10
35 21 0.10
36 34 0.16
37 56 0.27
38 59 0.28
39 15 0.07
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (37 bp):
TGTTTTCAAAACTATATAATATATGTTTTCAAAAATG
Found at i:1678909 original size:73 final size:72
Alignment explanation
Indices: 1678755--1678920 Score: 178
Period size: 73 Copynumber: 2.3 Consensus size: 72
1678745 CAAAAATGTG
* * * *
1678755 TTTTC-AAAACTATATAATATATGTTTTCGAAAACGTGTTTTCAAAACCATATTATATATTTTCA
1 TTTTCAAAAACTATATAATATATGCTTTCAAAAACGTGTTTTAAAAACCATATCATATATTTTCA
1678819 AAAACTAA
66 AAAAC-AA
* * * *
1678827 TTTTTAAAAACTATATATTATATGCTTTCAAAAAACGT-TTTCTAAAAACTATATAGCATATGTT
1 TTTTCAAAAACTATATAATATATGCTTTC-AAAAACGTGTTT-TAAAAACCATAT--CATATATT
1678891 TTCAAAAA-AA
62 TTCAAAAACAA
*
1678901 -TTTCAAAAACTATATTATAT
1 TTTTCAAAAACTATATAATAT
1678921 TATTATATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
72 4 0.05
73 41 0.53
74 19 0.24
76 14 0.18
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.40
Consensus pattern (72 bp):
TTTTCAAAAACTATATAATATATGCTTTCAAAAACGTGTTTTAAAAACCATATCATATATTTTCA
AAAACAA
Found at i:1679164 original size:20 final size:20
Alignment explanation
Indices: 1679139--1679206 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1679129 GCGCGCGCGG
1679139 TATTATTATTATCTTTATAT
1 TATTATTATTATCTTTATAT
*
1679159 TATTATTA-TATTTTTATA-
1 TATTATTATTATCTTTATAT
*
1679177 TATT-TTCTT-TCTTTTATATT
1 TATTATTATTATC-TTTATA-T
*
1679197 TATTACTATT
1 TATTATTATT
1679207 TTTTAGTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.08
18 11 0.29
19 9 0.24
20 12 0.32
21 3 0.08
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTATTATTATCTTTATAT
Found at i:1679259 original size:19 final size:17
Alignment explanation
Indices: 1679218--1679260 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1679208 TTTAGTATAT
*
1679218 TTATATTATTATTAGTA
1 TTATATTATTAATAGTA
1679235 TT-TATTATTAATATGTA
1 TTATATTATTAATA-GTA
1679252 TATATATTA
1 T-TATATTA
1679261 AATACACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.45
17 6 0.27
18 1 0.05
19 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
TTATATTATTAATAGTA
Found at i:1679985 original size:19 final size:19
Alignment explanation
Indices: 1679958--1680007 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1679948 TGTAAAGGTT
1679958 AATTCTTAAATT-ATTATTTA
1 AATT-TTAAATTGATT-TTTA
1679978 AATTTTAAATTGATTTTTA
1 AATTTTAAATTGATTTTTA
* *
1679997 AGTTTAAAATT
1 AATTTTAAATT
1680008 TGTAATTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
AATTTTAAATTGATTTTTA
Found at i:1680899 original size:22 final size:22
Alignment explanation
Indices: 1680871--1680919 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1680861 GACGATACGG
* *
1680871 GGACGGTCGGGGTACGTATCGT
1 GGACGGTCGAGGTACGTACCGT
1680893 GGACGGTCGAGGTACGTACCGT
1 GGACGGTCGAGGTACGTACCGT
1680915 GGACG
1 GGACG
1680920 AGCCACTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.45, T:0.18
Consensus pattern (22 bp):
GGACGGTCGAGGTACGTACCGT
Found at i:1682056 original size:75 final size:75
Alignment explanation
Indices: 1681968--1682124 Score: 208
Period size: 75 Copynumber: 2.1 Consensus size: 75
1681958 CAGTCTTAAT
* * ** * *
1681968 ATTTGATACTTTAATATTATGGTTTGA-TTATGGATTTTATTATTCTAGAGTTAATATTGTGATT
1 ATTTGACACTTTAATATTATGATTT-ATTTATAAATTTTATTATTCTAAACTTAATATTGTGATT
1682032 TGAATCTTGAG
65 TGAATCTTGAG
* *
1682043 ATTTGACATTTTAATATTATGATTTATTTATAAATTTTATTATTCTAAACTTAATATTGTGGTTT
1 ATTTGACACTTTAATATTATGATTTATTTATAAATTTTATTATTCTAAACTTAATATTGTGATTT
* *
1682108 GAGTCTTGAT
66 GAATCTTGAG
1682118 ATTTGAC
1 ATTTGAC
1682125 TTTATTTATA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 1 0.01
75 70 0.99
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (75 bp):
ATTTGACACTTTAATATTATGATTTATTTATAAATTTTATTATTCTAAACTTAATATTGTGATTT
GAATCTTGAG
Found at i:1682140 original size:19 final size:20
Alignment explanation
Indices: 1682116--1682156 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1682106 TTGAGTCTTG
*
1682116 ATATTTGAC-TTTATTTATA
1 ATATTTGACATCTATTTATA
*
1682135 ATATTTTACATCTATTTATA
1 ATATTTGACATCTATTTATA
1682155 AT
1 AT
1682157 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATTTGACATCTATTTATA
Found at i:1682168 original size:18 final size:19
Alignment explanation
Indices: 1682126--1682169 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1682116 ATATTTGACT
* *
1682126 TTATTTATAATATTTTACA
1 TTATTTATAATATTTAAAA
1682145 TCTATTTATAAT-TTTAAAA
1 T-TATTTATAATATTTAAAA
1682164 TTATTT
1 TTATTT
1682170 TATATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 7 0.32
20 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTATAATATTTAAAA
Found at i:1682248 original size:12 final size:12
Alignment explanation
Indices: 1682231--1682255 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1682221 TTTTCTGTCC
1682231 CCGTCCCCGTAT
1 CCGTCCCCGTAT
1682243 CCGTCCCCGTAT
1 CCGTCCCCGTAT
1682255 C
1 C
1682256 GGTGCAACAT
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:0.08, C:0.52, G:0.16, T:0.24
Consensus pattern (12 bp):
CCGTCCCCGTAT
Found at i:1683578 original size:16 final size:17
Alignment explanation
Indices: 1683539--1683587 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
1683529 GTTGCCTTGA
*
1683539 GATGATGACTGTGTGGT
1 GATGATGGCTGTGTGGT
**
1683556 GGCGATGGCT-TGTGGT
1 GATGATGGCTGTGTGGT
1683572 GATGATGG-TG-GTGGT
1 GATGATGGCTGTGTGGT
1683587 G
1 G
1683588 GTGGTGGTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 7 0.27
16 12 0.46
17 7 0.27
ACGTcount: A:0.12, C:0.06, G:0.49, T:0.33
Consensus pattern (17 bp):
GATGATGGCTGTGTGGT
Found at i:1683583 original size:3 final size:3
Alignment explanation
Indices: 1683567--1683600 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1683557 GCGATGGCTT
* *
1683567 GTG GTG ATG ATG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1683601 CGGCGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.06, C:0.00, G:0.62, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:1685409 original size:3 final size:3
Alignment explanation
Indices: 1685401--1685456 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
1685391 ACATTAGTTA
*
1685401 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1685448 TAT T-T TAT T
1 TAT TAT TAT T
1685457 TTTTATTTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1691806 original size:20 final size:21
Alignment explanation
Indices: 1691781--1691819 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1691771 AGAAACGAAA
*
1691781 AAACAATTAGAA-AAAAATGG
1 AAACAACTAGAATAAAAATGG
1691801 AAACAACTAGAATAAAAAT
1 AAACAACTAGAATAAAAAT
1691820 TCGGGCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (21 bp):
AAACAACTAGAATAAAAATGG
Found at i:1698428 original size:20 final size:19
Alignment explanation
Indices: 1698405--1698445 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
1698395 AGAAATAAAT
1698405 AAAAT-GGAAAAATTAAAGAA
1 AAAATGGGAAAAA--AAAGAA
1698425 AAAATGGGAAAAAAAAGAA
1 AAAATGGGAAAAAAAAGAA
1698444 AA
1 AA
1698446 CAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATGGGAAAAAAAAGAA
Found at i:1698444 original size:9 final size:9
Alignment explanation
Indices: 1698375--1698462 Score: 52
Period size: 9 Copynumber: 9.2 Consensus size: 9
1698365 GAAGAAAAAT
*
1698375 AAAAAATAA
1 AAAAAAGAA
1698384 GAAAAAAGAA
1 -AAAAAAGAA
* *
1698394 AAGAAATAA
1 AAAAAAGAA
*
1698403 ATAAAATGGAA
1 A-AAAA-AGAA
1698414 AAATTAAAGAA
1 AAA--AAAGAA
**
1698425 AAAATGGGAA
1 AAAA-AAGAA
1698435 AAAAAAGAA
1 AAAAAAGAA
*
1698444 AACAAAG-A
1 AAAAAAGAA
1698452 AAAAAAGAA
1 AAAAAAGAA
1698461 AA
1 AA
1698463 TGAGAATAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
8 7 0.12
9 21 0.36
10 20 0.34
11 9 0.15
12 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:1698478 original size:28 final size:27
Alignment explanation
Indices: 1698366--1698478 Score: 65
Period size: 28 Copynumber: 4.1 Consensus size: 27
1698356 ACTTCGCCTG
* *
1698366 AAGAAAAATAA-AAAATAAGAAAAAAGAA
1 AAGAAAAA-AAGAAAATGAG-AAAAATAA
* * *
1698394 AAGAAATAAATAAAATG-GAAAAATTA
1 AAGAAAAAAAGAAAATGAGAAAAATAA
* *
1698420 AAGAAAAAATGGGAAAA--A-AAAGAAAACA
1 AAGAAAAAA--AGAAAATGAGAAA-AATA-A
1698448 AAGAAAAAAAGAAAATGAGAATAAATAA
1 AAGAAAAAAAGAAAATGAGAA-AAATAA
1698476 AAG
1 AAG
1698479 GGGGATCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
26 22 0.34
27 5 0.08
28 31 0.48
29 5 0.08
30 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.10
Consensus pattern (27 bp):
AAGAAAAAAAGAAAATGAGAAAAATAA
Found at i:1703128 original size:15 final size:15
Alignment explanation
Indices: 1703104--1703146 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1703094 GCATCATTAA
*
1703104 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
1703119 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
*
1703134 ACTAAATATATAA
1 ATTAAAT-TATAA
1703147 TTATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:1703638 original size:177 final size:178
Alignment explanation
Indices: 1703339--1703696 Score: 531
Period size: 177 Copynumber: 2.0 Consensus size: 178
1703329 TGTCGTTAAA
*
1703339 TATTAATGGAGGAGAAGATGTAGAAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATTA
1 TATTAATAGAGGAGAAGATGTAGAAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATTA
*
1703404 ATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTTAATCATCAATCAGA
66 ATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTGAATCATCAATCAGA
* *
1703469 TGATGATATATATCACCATTTGATTAGA-TTTTTTAATATTGTTTATT
131 TGATGACATATATCACCATGTGATTAGATTTTTTTAATATTGTTTATT
* * *
1703516 TATTAATAGAGGAGATGATGTAGCAA-TTAATAAAATTTATATACTTATACATTTAGTCCTCATT
1 TATTAATAGAGGAGAAGATGTAG-AAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATT
* * * *
1703580 ACTTACACATTTTATTAATTTGGTCCTAACTTTTATTTAATTCAATAAATTGAATCATCAATCTG
65 AATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTGAATCATCAATCAG
* * ** * *
1703645 ATGGTGACATGTATCACTGTGTGATTGGATTTTTTTTAATATTTTTTATT
130 ATGATGACATATATCACCATGTGATTAGA-TTTTTTTAATATTGTTTATT
1703695 TA
1 TA
1703697 ATAAATTTTC
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
177 139 0.86
178 2 0.01
179 20 0.12
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (178 bp):
TATTAATAGAGGAGAAGATGTAGAAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATTA
ATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTGAATCATCAATCAGA
TGATGACATATATCACCATGTGATTAGATTTTTTTAATATTGTTTATT
Found at i:1705062 original size:15 final size:15
Alignment explanation
Indices: 1705039--1705072 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1705029 CCCTAAAAAC
*
1705039 TAATATTTTATAATT
1 TAATATTTTATAAAT
*
1705054 TAATGTTTTATAAAT
1 TAATATTTTATAAAT
1705069 TAAT
1 TAAT
1705073 TTAATGGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TAATATTTTATAAAT
Found at i:1713360 original size:60 final size:60
Alignment explanation
Indices: 1713263--1713375 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
1713253 AGATTCCTTA
*
1713263 ACTATAGGACATTACTTTGTTAAGTCTATCAACTATTAAAAGTTA-CAATATGACCTTCTG
1 ACTATAGGACATTACTTTGTTAAATCTATCAACTATTAAAAGTTATCAA-ATGACCTTCTG
* * * * *
1713323 ACTATATGACATTACTTTGTTAAATTTTTCGATTATTAAAAGTTATCAAATGA
1 ACTATAGGACATTACTTTGTTAAATCTATCAACTATTAAAAGTTATCAAATGA
1713376 TCAGCTGACT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (60 bp):
ACTATAGGACATTACTTTGTTAAATCTATCAACTATTAAAAGTTATCAAATGACCTTCTG
Found at i:1716408 original size:15 final size:14
Alignment explanation
Indices: 1716385--1716421 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1716375 TGTTTTACTT
1716385 TCATTTTATTTTGG
1 TCATTTTATTTTGG
*
1716399 TCACTTTTATTTTTG
1 TCA-TTTTATTTTGG
1716414 TCATTTTA
1 TCATTTTA
1716422 CTATGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.65
Consensus pattern (14 bp):
TCATTTTATTTTGG
Found at i:1717390 original size:139 final size:138
Alignment explanation
Indices: 1717229--1717527 Score: 395
Period size: 139 Copynumber: 2.1 Consensus size: 138
1717219 TTTTAAGTTT
* * * *
1717229 AGTCTAATAGTTGATTAAAATTGACTAGGTTAATAATTAAAGCTTCCAT-TTTAGGTTTAATTTC
1 AGTC-AATAATTGATTAAAATTGACTAGGTTAATAATT--AGATACCATGTTTAGGTTTAATTTA
* * * *
1717293 AAACTTAGTCTTTAAATTTAGGGGAAATTTTAATTTGTTCCTCACTTTTGCTCGATGTTTCA-TT
63 AAACTTAGTCCTTAAATTTAGGGGAAATTTTAATTTGGTACTCACTTTTGCTCGATGTTCCATTT
1717357 TTAATTATTCG
128 TTAATTATTCG
* * *
1717368 AGTCAAATGATTGATTAAAATTGACTAGGTTAATGATTAGATACTATGGTTTAGGTTTAATTTAA
1 AGTC-AATAATTGATTAAAATTGACTAGGTTAATAATTAGATACCAT-GTTTAGGTTTAATTTAA
* * *
1717433 AACTTAGTCCTTAAATTTAGGGGAATTTTTAATTTGGTACTCGCTTTTGCTTGATGTTCCATTTT
64 AACTTAGTCCTTAAATTTAGGGGAAATTTTAATTTGGTACTCACTTTTGCTCGATGTTCCATTTT
1717498 TAATTATTCG
129 TAATTATTCG
* *
1717508 ATTCAATAATTTATTAAAAT
1 AGTCAATAATTGATTAAAAT
1717528 GGTTTGGATT
Statistics
Matches: 139, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
137 6 0.04
139 117 0.84
140 16 0.12
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (138 bp):
AGTCAATAATTGATTAAAATTGACTAGGTTAATAATTAGATACCATGTTTAGGTTTAATTTAAAA
CTTAGTCCTTAAATTTAGGGGAAATTTTAATTTGGTACTCACTTTTGCTCGATGTTCCATTTTTA
ATTATTCG
Found at i:1720139 original size:33 final size:33
Alignment explanation
Indices: 1720100--1720165 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1720090 TAGTACGGAT
1720100 GGTGGACACGACCTTATGTGTCATACGGATTAG
1 GGTGGACACGACCTTATGTGTCATACGGATTAG
1720133 GGTGGACACGACCTTATGTGTCATACGGATTAG
1 GGTGGACACGACCTTATGTGTCATACGGATTAG
1720166 CACTATGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (33 bp):
GGTGGACACGACCTTATGTGTCATACGGATTAG
Found at i:1721841 original size:18 final size:18
Alignment explanation
Indices: 1721815--1721851 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1721805 ATGTTTAATG
1721815 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
*
1721833 AAAAGGATACCAATTGTT
1 AAAAAGATACCAATTGTT
1721851 A
1 A
1721852 CCAATGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:1721854 original size:28 final size:29
Alignment explanation
Indices: 1721822--1721889 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
1721812 ATGAAAAAGA
* *
1721822 TACCAATTGTTAAAAGGATA-CCAATTGT
1 TACCAATTGTTAAAAAGAAACCCAATTGT
*
1721850 TACCAATGGTTAAAAAGAAACCCAATTGT
1 TACCAATTGTTAAAAAGAAACCCAATTGT
1721879 TACCAATTGTT
1 TACCAATTGTT
1721890 GGAAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (29 bp):
TACCAATTGTTAAAAAGAAACCCAATTGT
Found at i:1721875 original size:29 final size:28
Alignment explanation
Indices: 1721822--1721885 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
1721812 ATGAAAAAGA
* * *
1721822 TACCAATTGTTAAAAGGATACCAATTGT
1 TACCAATGGTTAAAAAGAAACCAATTGT
1721850 TACCAATGGTTAAAAAGAAACCCAATTGT
1 TACCAATGGTTAAAAAGAAA-CCAATTGT
1721879 TACCAAT
1 TACCAAT
1721886 TGTTGGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (28 bp):
TACCAATGGTTAAAAAGAAACCAATTGT
Found at i:1728497 original size:20 final size:20
Alignment explanation
Indices: 1728472--1728509 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1728462 CCCCCTTTGA
*
1728472 AGGGGAACCGATTCCCCCCT
1 AGGGGAACCGATACCCCCCT
*
1728492 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1728510 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.37, G:0.26, T:0.13
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCCT
Found at i:1728510 original size:19 final size:20
Alignment explanation
Indices: 1728472--1728514 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1728462 CCCCCTTTGA
*
1728472 AGGGGAACCGATTCCCCCCT
1 AGGGGAACCGATTACCCCCT
*
1728492 AGGGGAATCGA-TACCCCCT
1 AGGGGAACCGATTACCCCCT
1728511 -GGGG
1 AGGGG
1728515 TTCTGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 7 0.33
20 10 0.48
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (20 bp):
AGGGGAACCGATTACCCCCT
Found at i:1734132 original size:33 final size:33
Alignment explanation
Indices: 1734072--1734134 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1734062 TTTACAAACA
* *
1734072 CCCTAGTTTTTCACGGGTTAAACTAGAACCTTT
1 CCCTAGCTTTTCACGGGTCAAACTAGAACCTTT
*
1734105 CCCTAGCTTTTCACGGGATCAGA-TAGAACC
1 CCCTAGCTTTTCACGGG-TCAAACTAGAACC
1734135 AAAACCCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (33 bp):
CCCTAGCTTTTCACGGGTCAAACTAGAACCTTT
Found at i:1734686 original size:20 final size:20
Alignment explanation
Indices: 1734661--1734714 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1734651 CCTTGTCTAT
*
1734661 GGTATCGATACTATAT-GTAG
1 GGTATCGATACTAT-TCATAG
*
1734681 GGTATCGATACTCATTCATAT
1 GGTATCGATACT-ATTCATAG
1734702 GGTATCGATACTA
1 GGTATCGATACTA
1734715 CATGAAGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
GGTATCGATACTATTCATAG
Found at i:1734707 original size:21 final size:20
Alignment explanation
Indices: 1734658--1734714 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1734648 TACCCTTGTC
*
1734658 TATGGTATCGATACTATATG
1 TATGGTATCGATACTATATA
*
1734678 TAGGGTATCGATACTCAT-TCA
1 TATGGTATCGATACT-ATAT-A
1734699 TATGGTATCGATACTA
1 TATGGTATCGATACTA
1734715 CATGAAGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (20 bp):
TATGGTATCGATACTATATA
Found at i:1737430 original size:2 final size:2
Alignment explanation
Indices: 1737423--1737565 Score: 286
Period size: 2 Copynumber: 71.5 Consensus size: 2
1737413 ATACGTCTAT
1737423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1737465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1737507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1737549 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1737566 TTAATTACTC
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 141 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1749335 original size:45 final size:45
Alignment explanation
Indices: 1749270--1749364 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
1749260 GCATACAATC
* * * *
1749270 ATGACACACAAATGTGTGTCATCTTT-TTTGATGACGTGTGCTTCA
1 ATGACAAACAAATGTATGTCATCTTTATTT-ATGACGGGGGCTTCA
*
1749315 ATGACAAACAAATGTATGTCATCTTTATTTATGGCGGGGGCTTCA
1 ATGACAAACAAATGTATGTCATCTTTATTTATGACGGGGGCTTCA
1749360 ATGAC
1 ATGAC
1749365 CCGCAATGCG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 41 0.93
46 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (45 bp):
ATGACAAACAAATGTATGTCATCTTTATTTATGACGGGGGCTTCA
Found at i:1749391 original size:13 final size:13
Alignment explanation
Indices: 1749369--1749399 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1749359 AATGACCCGC
*
1749369 AATGCGTGTCATA
1 AATGCCTGTCATA
1749382 AATGCCTGTCATA
1 AATGCCTGTCATA
1749395 AATGC
1 AATGC
1749400 GCATCATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (13 bp):
AATGCCTGTCATA
Found at i:1750457 original size:17 final size:18
Alignment explanation
Indices: 1750422--1750464 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1750412 TTGGGGACTC
*
1750422 AAAAAGTATTTGTCATTTA
1 AAAAAATATTTGT-ATTTA
1750441 AAAAAATATTTGT-TTTA
1 AAAAAATATTTGTATTTA
1750458 ATAAAAA
1 A-AAAAA
1750465 AACAAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 5 0.23
19 12 0.55
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (18 bp):
AAAAAATATTTGTATTTA
Found at i:1751817 original size:28 final size:28
Alignment explanation
Indices: 1751784--1751853 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
1751774 ACAAAGAATA
*
1751784 AAAATAAATAAAATATG-A-GGACTAAATT
1 AAAATAAATAAAAT-TGCATGG-CCAAATT
1751812 AAAATAAACTAAAATTGCATGGCCAAATT
1 AAAATAAA-TAAAATTGCATGGCCAAATT
*
1751841 AGAATAAATAAAA
1 AAAATAAATAAAA
1751854 AATAGATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 15 0.41
29 20 0.54
30 2 0.05
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (28 bp):
AAAATAAATAAAATTGCATGGCCAAATT
Found at i:1753244 original size:3 final size:3
Alignment explanation
Indices: 1753238--1753321 Score: 125
Period size: 3 Copynumber: 28.0 Consensus size: 3
1753228 ATAAAAAAAT
1753238 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
* * *
1753286 ATA GTA ATA ATA ATA A-A ACAA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
1753322 TTTTCGGGAT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
2 2 0.03
3 70 0.95
4 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1753777 original size:132 final size:132
Alignment explanation
Indices: 1753496--1753955 Score: 579
Period size: 132 Copynumber: 3.5 Consensus size: 132
1753486 CGAGAAACGA
* *
1753496 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGG-AAGACTTGTTCCACTGCTACTCAG
1 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAA-ACTTGTTCCACTGTTCCTCAG
* * * ** * * *
1753560 GAAAGATCAAATGTTGAAAGATAGGGATCTGTTCCGCTACTTCTTGAGGGAAAATCAGATCTA-A
65 GGAAGATCAAAT-CTGAAA-AAAATGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGATCTAGG
*
1753624 AAATGT
128 GAA-GT
* * *
1753630 TGATTCA-TTCAACTGTTCTTTTA-GGAAGATTGAATCGAGGTAAACTTGTTCCAATGTTCCTTA
1 TGATTCATTTC-ACTGTTC-TTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCTCA
1753693 GGGAAGATCAAATCTGAAAAAAATGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGATCTAGGG
64 GGGAAGATCAAATCTGAAAAAAATGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGATCTAGGG
1753758 AAGT
129 AAGT
* *
1753762 TGATTCATTTCACTGTTCTTCAAGGAAGACTGAATCGAGGTAAACTTGTTCCACTGTTCCTCAGG
1 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCTCAGG
** ** * *
1753827 GAAGATCAAATCTGAAAAAAATGGATCTAATTCATTGTTTCTTGAGGGAAAATCAGATCTGGGGA
66 GAAGATCAAATCTGAAAAAAAT-GATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGATCTAGGGA
1753892 CA-T
130 -AGT
* * * *
1753895 TGATTCATTGCTCTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTATTCCACTGTTCCT
1 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCT
1753956 AAAGGAAAAT
Statistics
Matches: 288, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
131 3 0.01
132 115 0.40
133 105 0.36
134 60 0.21
135 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (132 bp):
TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCTCAGG
GAAGATCAAATCTGAAAAAAATGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGATCTAGGGAA
GT
Found at i:1753922 original size:133 final size:132
Alignment explanation
Indices: 1753496--1754064 Score: 576
Period size: 134 Copynumber: 4.3 Consensus size: 132
1753486 CGAGAAACGA
* *
1753496 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGG-AAGACTTGTTCCACTGCTACTCAG
1 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAA-ACTTGTTCCACTGTTCCTCAG
* * * * * * *
1753560 GAAAGATCAAATGTTGAAAGATAGGGATCTGTTCCGCTACTTCTTGAGGGAAAATCAGATCTA-A
65 GGAAGATCAAAT-CTGAAAAAAAGGGATCTGTTCCACTGCTTCTTGAGGGAAAATCAGATCTAGG
*
1753624 AAATGT
129 GAA--T
* * *
1753630 TGATTCA-TTCAACTGTTCTTTTA-GGAAGATTGAATCGAGGTAAACTTGTTCCAATGTTCCTTA
1 TGATTCATTTC-ACTGTTC-TTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCTCA
* * *
1753693 GGGAAGATCAAATCTGAAAAAAA-TGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGATCTAGG
64 GGGAAGATCAAATCTGAAAAAAAGGGATCTGTTCCACTGCTTCTTGAGGGAAAATCAGATCTAGG
1753757 GAAGT
129 GAA-T
* *
1753762 TGATTCATTTCACTGTTCTTCAAGGAAGACTGAATCGAGGTAAACTTGTTCCACTGTTCCTCAGG
1 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCTCAGG
* * * * *
1753827 GAAGATCAAATCTGAAAAAAATGGATCTAATT-CATTGTTTCTTGAGGGAAAATCAGATCTGGGG
66 GAAGATCAAATCTGAAAAAAAGGGATCT-GTTCCACTGCTTCTTGAGGGAAAATCAGATCTAGGG
1753891 ACAT
130 A-AT
* * * * * *
1753895 TGATTCATTGCTCTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTATTCCACTGTTCCTAAAG
1 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCTCAGG
* * * * * * * * * *
1753960 GAAAATTAAATTTGGAAAAAGAGGGATATGTTCCATTGTTTATTGAGGGAAAATAAGATAT-GGA
66 GAAGATCAAATCT-GAAAAAAAGGGATCTGTTCCACTGCTTCTTGAGGGAAAATCAGATCTAGG-
*
1754024 AAAGT
129 GAA-T
* * * * *
1754029 TGATTTATTCCATTGTTCTTCAGGGAAAATTAAATC
1 TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATC
1754065 AAGTTCGATT
Statistics
Matches: 373, Mismatches: 49, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
131 3 0.01
132 112 0.30
133 122 0.33
134 131 0.35
135 5 0.01
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (132 bp):
TGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCACTGTTCCTCAGG
GAAGATCAAATCTGAAAAAAAGGGATCTGTTCCACTGCTTCTTGAGGGAAAATCAGATCTAGGGA
AT
Found at i:1761623 original size:12 final size:12
Alignment explanation
Indices: 1761621--1761674 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
1761611 TTATTCATTT
1761621 TTTTCTTTTTTCA
1 TTTT-TTTTTTCA
1761634 TTTTTTTTTTCA
1 TTTTTTTTTTCA
1761646 ---TTTTTTTCA
1 TTTTTTTTTTCA
1761655 TTTTTTTTTTCA
1 TTTTTTTTTTCA
1761667 TTTTTTTT
1 TTTTTTTT
1761675 CATTTTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.24
12 25 0.66
13 4 0.11
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:1761629 original size:20 final size:19
Alignment explanation
Indices: 1761601--1761673 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 19
1761591 TTGAACCTTC
*
1761601 TTTTGTTTTTTTATTCATTT
1 TTTTCTTTTTTTATT-ATTT
* *
1761621 TTTTCTTTTTTCATTTTTT
1 TTTTCTTTTTTTATTATTT
*
1761640 TTTTCATTTTTTTCATTTTTT
1 TTTTC-TTTTTTT-ATTATTT
1761661 TTTTCATTTTTTT
1 TTTTC-TTTTTTT
1761674 TCATTTTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 8 0.17
20 19 0.40
21 20 0.43
ACGTcount: A:0.08, C:0.08, G:0.01, T:0.82
Consensus pattern (19 bp):
TTTTCTTTTTTTATTATTT
Found at i:1761642 original size:21 final size:21
Alignment explanation
Indices: 1761618--1761685 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
1761608 TTTTTATTCA
1761618 TTTTTTTC--TTTTTTCATTT
1 TTTTTTTCTTTTTTTTCATTT
*
1761637 TTTTTTTCATTTTTTTCATTT
1 TTTTTTTCTTTTTTTTCATTT
1761658 TTTTTTTCATTTTTTTTCATTT
1 TTTTTTTC-TTTTTTTTCATTT
*
1761680 TCTTTT
1 TTTTTT
1761686 ATTATTTACC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 8 0.18
21 19 0.43
22 17 0.39
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTTCATTT
Found at i:1761645 original size:28 final size:29
Alignment explanation
Indices: 1761606--1761680 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
1761596 CCTTCTTTTG
*
1761606 TTTTTTTATTCATTTTTTTC-TTTTTTCA
1 TTTTTTTTTTCATTTTTTTCATTTTTTCA
**
1761634 TTTTTTTTTTCATTTTTTTCATTTTTTTT
1 TTTTTTTTTTCATTTTTTTCATTTTTTCA
1761663 TTCATTTTTTTTCATTTT
1 TT--TTTTTTTTCATTTT
1761681 CTTTTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 19 0.46
29 8 0.20
31 14 0.34
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (29 bp):
TTTTTTTTTTCATTTTTTTCATTTTTTCA
Found at i:1761681 original size:28 final size:28
Alignment explanation
Indices: 1761606--1761685 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 28
1761596 CCTTCTTTTG
*
1761606 TTTTTTTATTCATTTT-TTTCTTTTTTCA
1 TTTTTTT-TTCATTTTCTTTTTTTTTTCA
1761634 TTTTTTTTTTCATTTTTTTCATTTTTTTTTTCA
1 -TTTTTTTTTCA---TTTTC-TTTTTTTTTTCA
1761667 -TTTTTTTTCATTTTCTTTT
1 TTTTTTTTTCATTTTCTTTT
1761686 ATTATTTACC
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
27 4 0.09
28 9 0.20
29 7 0.16
31 14 0.31
33 11 0.24
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTTTTTTTCATTTTCTTTTTTTTTTCA
Found at i:1761685 original size:12 final size:11
Alignment explanation
Indices: 1761626--1761685 Score: 72
Period size: 12 Copynumber: 5.5 Consensus size: 11
1761616 CATTTTTTTC
1761626 TTTTTTCATTTT
1 TTTTTTCA-TTT
1761638 TTTTTTCA--T
1 TTTTTTCATTT
1761647 TTTTTTCATTTT
1 TTTTTTCA-TTT
1761659 TTTTTTCA-TT
1 TTTTTTCATTT
1761669 TTTTTTCATTT
1 TTTTTTCATTT
*
1761680 TCTTTT
1 TTTTTT
1761686 ATTATTTACC
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 9 0.21
10 10 0.23
11 7 0.16
12 17 0.40
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:1767200 original size:19 final size:19
Alignment explanation
Indices: 1767176--1767232 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
1767166 CCGAAACCGA
1767176 TTTTTTCGGTTCGGTTCGG
1 TTTTTTCGGTTCGGTTCGG
*
1767195 TTTTTT---TAACGGTTCGG
1 TTTTTTCGGT-TCGGTTCGG
1767212 TTTTTTCGGTTCGGTTCGG
1 TTTTTTCGGTTCGGTTCGG
1767231 TT
1 TT
1767233 CAGTTTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.03
17 14 0.44
19 16 0.50
20 1 0.03
ACGTcount: A:0.04, C:0.14, G:0.28, T:0.54
Consensus pattern (19 bp):
TTTTTTCGGTTCGGTTCGG
Found at i:1767385 original size:25 final size:26
Alignment explanation
Indices: 1767368--1767420 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
1767358 AAATGAAGCC
1767368 TTTAAA-CCAAACCGAAAACGAACCG
1 TTTAAAGCCAAACCGAAAACGAACCG
*
1767393 TTTAAAGCCAAACCG-AACCGAACCG
1 TTTAAAGCCAAACCGAAAACGAACCG
1767418 TTT
1 TTT
1767421 TACTCGATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.17
Consensus pattern (26 bp):
TTTAAAGCCAAACCGAAAACGAACCG
Found at i:1773240 original size:131 final size:131
Alignment explanation
Indices: 1772872--1773240 Score: 411
Period size: 131 Copynumber: 2.8 Consensus size: 131
1772862 ATAATTTTAA
* *
1772872 GAGAGAAAACGATAATATCTAATTATTTTCAATCGAAAATAAATGACCTTTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAACA
* * * ** *
1772937 GTCATTTATTAC-TCTAATCAAAATGAAGATATCTTACTATTTTGTCTTAAAATTCAATATCGAT
66 GTCATTTATTACTTC-AATCGAAATGAAAATATATTACTATTCCGTCTTAAAAATCAATATCGAT
1773001 TC
130 TC
* * * * * * * *
1773003 AAGTGAAAATGATAATATCTAATGATTTCCAACCGATAATAAATGACCTCTCATACCTTAAACCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAACA
* * * * * *
1773068 GTCATTTATTGCTCCAATCGAAATGAATAGATATCACTATTCCGTCTTAAAAATCAATATTGATT
66 GTCATTTATTACTTCAATCGAAATGAAAATATATTACTATTCCGTCTTAAAAATCAATATCGATT
1773133 C
131 C
* * * * * **
1773134 GAGAGAAAACGGTAAAAT-TGAATTATTTCCAATCGAGAATAAAAGACATCTCATGCCTTAAAGT
1 GAGAGAAAACGATAATATCT-AATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAAC
* *
1773198 AGTAATTTATTACTTCAA-CTGAAATGAAAATATATTATTATTC
65 AGTCATTTATTACTTCAATC-GAAATGAAAATATATTACTATTC
1773241 TGAATATCGA
Statistics
Matches: 194, Mismatches: 41, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
130 2 0.01
131 191 0.98
132 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAACA
GTCATTTATTACTTCAATCGAAATGAAAATATATTACTATTCCGTCTTAAAAATCAATATCGATT
C
Found at i:1773720 original size:5 final size:5
Alignment explanation
Indices: 1773710--1773748 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
1773700 ATGTAAAACT
*
1773710 TAAAA TAAAA TAAAA TAAAA TGAAAA TAAGAC TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAA-AA TAAAA TA
1773749 TAAACAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:1773728 original size:22 final size:23
Alignment explanation
Indices: 1773703--1773753 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1773693 AAGCAACATG
*
1773703 TAAAACTTAAAATAA-AATAAAA
1 TAAAACTGAAAATAAGAATAAAA
*
1773725 TAAAA-TGAAAATAAGACTAAAA
1 TAAAACTGAAAATAAGAATAAAA
1773747 TATAAAC
1 TA-AAAC
1773754 AATCAAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 8 0.33
22 13 0.54
23 3 0.12
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (23 bp):
TAAAACTGAAAATAAGAATAAAA
Found at i:1773737 original size:11 final size:10
Alignment explanation
Indices: 1773710--1773748 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1773700 ATGTAAAACT
1773710 TAAAATAAAA
1 TAAAATAAAA
1773720 TAAAATAAAA
1 TAAAATAAAA
*
1773730 TGAAAATAAGAC
1 T-AAAATAA-AA
1773742 TAAAATA
1 TAAAATA
1773749 TAAACAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 11 0.42
11 13 0.50
12 2 0.08
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:1775221 original size:12 final size:12
Alignment explanation
Indices: 1775206--1775231 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1775196 ATATATATAT
1775206 TAATATTAATAA
1 TAATATTAATAA
1775218 TAATATTAATAA
1 TAATATTAATAA
1775230 TA
1 TA
1775232 GTAAAGAAAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:1789609 original size:13 final size:13
Alignment explanation
Indices: 1789553--1789609 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
1789543 CTTAACAACA
1789553 ATATAATATAATAT
1 ATATAA-ATAATAT
*
1789567 ATATATAATAA-AC
1 ATATA-AATAATAT
*
1789580 A-ATAAATAATGT
1 ATATAAATAATAT
1789592 ATATAAATAATAT
1 ATATAAATAATAT
*
1789605 TTATA
1 ATATA
1789610 CTATATTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.14
12 4 0.11
13 16 0.46
14 9 0.26
15 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:1789771 original size:40 final size:37
Alignment explanation
Indices: 1789619--1789854 Score: 184
Period size: 40 Copynumber: 6.4 Consensus size: 37
1789609 ACTATATTTA
* *
1789619 TTTTAGAAAC-ATATACTATA--TTTT-CAAAACCA-
1 TTTTAAAAACTATATATTATATGTTTTCCAAAACCAT
* *
1789651 TTTTAAAAACTATATACTATATGCTTT-CAAAA--AT
1 TTTTAAAAACTATATATTATATGTTTTCCAAAACCAT
* * *
1789685 ATTTT-AAAACTATATATTATATGTTTTCAAAAATACGT
1 -TTTTAAAAACTATATATTATATGTTTTCCAAAA-CCAT
*
1789723 TTTCAAAAACTATATTATATATATGTTTTCCAAAACCGAT
1 TTTTAAAAACTATA-TAT-TATATGTTTTCCAAAACC-AT
* *
1789763 TTTTAAAAATCTATATATTATATTGCTTTCAAAAAACCAT
1 TTTTAAAAA-CTATATATTATA-TGTTTTC-CAAAACCAT
* * **
1789803 TTTCTAAAAGCTATATATTATATGTTTTTCAAAAATAT
1 TTT-TAAAAACTATATATTATATGTTTTCCAAAACCAT
* *
1789841 TTTCAAAGACTATA
1 TTTTAAAAACTATA
1789855 CTATATTATT
Statistics
Matches: 165, Mismatches: 22, Indels: 29
0.76 0.10 0.13
Matches are distributed among these distances:
32 9 0.05
33 11 0.07
34 20 0.12
35 16 0.10
37 11 0.07
38 19 0.12
39 13 0.08
40 50 0.30
41 16 0.10
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATGTTTTCCAAAACCAT
Found at i:1789785 original size:79 final size:77
Alignment explanation
Indices: 1789644--1789836 Score: 215
Period size: 79 Copynumber: 2.5 Consensus size: 77
1789634 CTATATTTTC
* *
1789644 AAAACCA-TTT-TAAAAACTATATACTATATGCTTT-CAAAA---ATATTTTAAAACTATATATT
1 AAAACCATTTTCTAAAAACTATATATTATATGTTTTCCAAAACCGAT-TTTTAAAACTATATATT
*
1789703 ATA-TGTTTTCAA
65 ATATTGCTTTCAA
*
1789715 AAATA-CGTTTTC-AAAAACTATATTATATATATGTTTTCCAAAACCGATTTTTAAAAATCTATA
1 AAA-ACCATTTTCTAAAAACTATA-TAT-TATATGTTTTCCAAAACCGATTTTT-AAAA-CTATA
1789778 TATTATATTGCTTTCAA
61 TATTATATTGCTTTCAA
* *
1789795 AAAACCATTTTCTAAAAGCTATATATTATATGTTTTTCAAAA
1 AAAACCATTTTCTAAAAACTATATATTATATGTTTTCCAAAA
1789837 ATATTTTCAA
Statistics
Matches: 101, Mismatches: 7, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
71 4 0.04
72 14 0.14
73 2 0.02
74 9 0.09
75 5 0.05
77 4 0.04
78 6 0.06
79 28 0.28
80 20 0.20
81 9 0.09
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.41
Consensus pattern (77 bp):
AAAACCATTTTCTAAAAACTATATATTATATGTTTTCCAAAACCGATTTTTAAAACTATATATTA
TATTGCTTTCAA
Found at i:1803365 original size:17 final size:17
Alignment explanation
Indices: 1803343--1803376 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1803333 AAATAGTAGT
1803343 GAAGCAAGATCAGATCA
1 GAAGCAAGATCAGATCA
1803360 GAAGCAAGATCAGATCA
1 GAAGCAAGATCAGATCA
1803377 AAAGTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (17 bp):
GAAGCAAGATCAGATCA
Found at i:1804850 original size:6 final size:6
Alignment explanation
Indices: 1804839--1804899 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
1804829 AATTATAGTA
*
1804839 ATTAAT ATTAAT ATTAAT ATTTTAATT ATTAAGT ATTACT A-TAAT ATTAAAT
1 ATTAAT ATTAAT ATTAAT A--TTAA-T ATTAA-T ATTAAT ATTAAT ATT-AAT
*
1804891 ATTTAT ATT
1 ATTAAT ATT
1804900 TTATATTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
5 4 0.09
6 21 0.46
7 15 0.33
8 4 0.09
9 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTAAT
Found at i:1807530 original size:20 final size:20
Alignment explanation
Indices: 1807470--1807540 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1807460 GGTAACGAAC
1807470 TTGACAAAACC-GATTGGAAA-
1 TTGACAAAACCAG-TT-GAAAT
* *
1807490 TTAACAAAACCGGTTGAAAT
1 TTGACAAAACCAGTTGAAAT
**
1807510 TTGACAAAACCAGTTTCAAT
1 TTGACAAAACCAGTTGAAAT
1807530 TTGACAAAACC
1 TTGACAAAACC
1807541 GGTAAAAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 4 0.09
20 39 0.89
21 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (20 bp):
TTGACAAAACCAGTTGAAAT
Found at i:1807843 original size:194 final size:197
Alignment explanation
Indices: 1807502--1808212 Score: 985
Period size: 194 Copynumber: 3.6 Consensus size: 197
1807492 AACAAAACCG
* *
1807502 GTTGAAATTTGACAAAACC-AGTTTCAATTTGACAAAACCGGTAAAAAGCTACC-GTAATTGTTG
1 GTTGAAATTTGACAAAACCGA-TTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAAATTGTTG
* * * *
1807565 AAATTTGTATAGATACGTTTATAAGTATATGTACCAAAGTATCAGTACTGTATGAATTTAAAAGA
65 AAATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGA
* *
1807630 ATTGCAATAACAACGGCTATAAAGTATCGATACC-T-ACACATGTATCGATACATGACAATATAA
130 ATTGCAATAATAGCGGCTATAAAGTATCGATACCTTAACACATGTATCGATACATGACAATATAA
1807693 CAT
195 CAT
* * * *
1807696 GTTGAAATTTGTCAAAACCGATTTCAATTTGAAAAAACCTGTAAAGAGCTACCAG-AATTTTTGA
1 GTTGAAATTTGACAAAACCGATTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAAATTGTTGA
* *
1807760 AATTTGTATCGATACGTTTATAAATGTATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAA
66 AATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAA
* * *
1807825 TTACAATAATAGCGGCTATAAAGTATCGATACCTTAGACATATGTATCGATACATGATAATATAA
131 TTGCAATAATAGCGGCTATAAAGTATCGATACCTTA-ACACATGTATCGATACATGACAATATAA
1807890 CAT
195 CAT
* * * * *
1807893 GTTTAAATTTGACAAAATCGGTTTCAATTTGACAAAACCGGTAAAGAACTA-CAGAAATGGTTGA
1 GTTGAAATTTGACAAAACCGATTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAAATTGTTGA
* * *
1807957 AATTTGTATCGAAACTTTTATAAGTATATGTACCAAAGTATTGGTAC-TTAGGAATTTAAAAGAA
66 AATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAA
* * * *
1808021 TTGCAATAATAGAGTCTATAAAGTATCAATACCTTAGACACATGTATCGATACTTGACAATATAA
131 TTGCAATAATAGCGGCTATAAAGTATCGATACCTTA-ACACATGTATCGATACATGACAATATAA
*
1808086 CAG
195 CAT
* * * *
1808089 GTTGAAATTTGACAAAATCAATTTCAATTTGACAAAACCGGTAAAGCGCTACC-GGAATTGTTGA
1 GTTGAAATTTGACAAAACCGATTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAAATTGTTGA
* * *
1808153 AA---GTATCGATATGTTTATAAGTATATGTACCATAGTATTGGTACTTTAGGAATTTAAAAG
66 AATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAG
1808213 TAATGAAAAA
Statistics
Matches: 460, Mismatches: 49, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
193 38 0.08
194 159 0.35
195 3 0.01
196 137 0.30
197 123 0.27
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (197 bp):
GTTGAAATTTGACAAAACCGATTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAAATTGTTGA
AATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAA
TTGCAATAATAGCGGCTATAAAGTATCGATACCTTAACACATGTATCGATACATGACAATATAAC
AT
Found at i:1807921 original size:20 final size:20
Alignment explanation
Indices: 1807893--1807934 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1807883 AATATAACAT
*
1807893 GTTTAAATTTGACAAAATCG
1 GTTTAAATTTGACAAAACCG
*
1807913 GTTTCAATTTGACAAAACCG
1 GTTTAAATTTGACAAAACCG
1807933 GT
1 GT
1807935 AAAGAACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (20 bp):
GTTTAAATTTGACAAAACCG
Found at i:1809429 original size:20 final size:21
Alignment explanation
Indices: 1809391--1809429 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1809381 TCCAAGTATC
*
1809391 GATACTTCTTATGCCAGTAAG
1 GATACTTCTTATGCAAGTAAG
*
1809412 GATACTT-TTATTCAAGTA
1 GATACTTCTTATGCAAGTA
1809430 TGATTCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
GATACTTCTTATGCAAGTAAG
Found at i:1809497 original size:146 final size:146
Alignment explanation
Indices: 1809120--1809487 Score: 506
Period size: 146 Copynumber: 2.5 Consensus size: 146
1809110 TGTTGATATC
*
1809120 GATACTTTTATTCCAGTAT-ACTTGTCAAACAATTTGAACACCAAATGTATCGATACACATTATT
1 GATACTTTTATTCCAGTATGA-TTGTCAAACAATTTGAACGCCAAATGTATCGATACACATTATT
* * *
1809184 AAAGTGTCGATATTTATAATTTCGAAAAAATGTATGCAAATTATGAAAATGTCCAAATATCGATA
65 AAAGTATCGATATTTATAATTTCGAAAAAATGTAAGCAAAGTATGAAAATGTCCAAATATCGATA
* *
1809249 CTTCTTACGCCGGTATG
130 CTTCTTACGCCAGTAAG
* * * * * *
1809266 GATACTTTAAATCCATTATGTTTGTCAAACAATTTGTAGGCCAAATGTATCGATACACATTATTA
1 GATACTTTTATTCCAGTATGATTGTCAAACAATTTGAACGCCAAATGTATCGATACACATTATTA
* * *
1809331 TAGTATCGATATTTATAATTTCGAAACAATGTAAGCAAAGTATGAAAATGTCCAAGTATCGATAC
66 AAGTATCGATATTTATAATTTCGAAAAAATGTAAGCAAAGTATGAAAATGTCCAAATATCGATAC
*
1809396 TTCTTATGCCAGTAAG
131 TTCTTACGCCAGTAAG
* * * * *
1809412 GATACTTTTATTCAAGTATGATTCTCAAACAATTTGCACGCAAAATGTATAGATACACA-TATAT
1 GATACTTTTATTCCAGTATGATTGTCAAACAATTTGAACGCCAAATGTATCGATACACATTAT-T
*
1809476 AAATTATCGATA
65 AAAGTATCGATA
1809488 CTTGGAATTT
Statistics
Matches: 192, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
145 3 0.02
146 189 0.98
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (146 bp):
GATACTTTTATTCCAGTATGATTGTCAAACAATTTGAACGCCAAATGTATCGATACACATTATTA
AAGTATCGATATTTATAATTTCGAAAAAATGTAAGCAAAGTATGAAAATGTCCAAATATCGATAC
TTCTTACGCCAGTAAG
Found at i:1809630 original size:20 final size:20
Alignment explanation
Indices: 1809585--1809622 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1809575 GTAAATACCA
*
1809585 AGTATCGATACTCTTTATAC
1 AGTATAGATACTCTTTATAC
1809605 AGGTATAGATACT-TTTAT
1 A-GTATAGATACTCTTTAT
1809623 TCCAGTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
AGTATAGATACTCTTTATAC
Found at i:1809748 original size:199 final size:199
Alignment explanation
Indices: 1809382--1810387 Score: 1301
Period size: 199 Copynumber: 5.0 Consensus size: 199
1809372 ATGAAAATGT
** * *
1809382 CCAAGTATCGATACTTCTTATGCCA-GTA-AGGATACTTTTATTCAAGTATGATTCTCAAACAAT
1 CCAAGTATCGATACTT-TTAT-ATAGGTATA-GATACTTTTATTCCAGTATGCTTCTCAAACAAT
** * * * *
1809445 TTGCACGCAAAATGTATAGATACACATATATAAATTATCGATACTTGGAATTTTGGATCCTATTA
63 TTGCACGCAAAATGTATCTATACACATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTA
* * * *
1809510 ATTTGAAGTAATAGGTAAATTAATAATGTAAACGGTAAAAGTCTGA-TGGTATAATGATAATAGG
128 CTTTAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTCT-ACCGGTATAATGATAATAGG
1809574 CGTAAATA
192 CGTAAATA
* * **
1809582 CCAAGTATCGATACTCTTTATACAGGTATAGATACTTTTATTCCAGTATGCTTCTCAAATAGCTT
1 CCAAGTATCGATACT-TTTATATAGGTATAGATACTTTTATTCCAGTATGCTTCTCAAACAATTT
** *
1809647 ATACGCAAAATGTATCTATGCACATATAT-AAGTATCGATACTTGGAATTTCGAAACCTATTACT
65 GCACGCAAAATGTATCTATACACATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACT
*
1809711 TTAAAGTAATAGGTAAATTAATAATGTAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGT
130 TTAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGT
1809776 AAATA
195 AAATA
* * * * *
1809781 CCAAGTAT-TAGTACTTTTATATAGGTAT-GAATAGTTTTATTCCAATATGTTTATCAAACAATT
1 CCAAGTATCGA-TACTTTTATATAGGTATAG-ATACTTTTATTCCAGTATGCTTCTCAAACAATT
* *
1809844 TGCACGTAAAATGTATCTATACACATATATAAAGTATCGATACTTGGAATTTCGAAACATATTAC
64 TGCACGCAAAATGTATCTATACACATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTAC
* *
1809909 TTTAAAGTAATAGGTAAAATAACAATGTAAACGGTAAAAGTCTACCGGTATAATGATAATAGACG
129 TTTAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCG
1809974 TAAATA
194 TAAATA
* * *
1809980 CCAAGTATCAATACTTTTATATAGGTATAGATTCTTTTATTCCAGTATGTTTCTCAAACAATTTG
1 CCAAGTATCGATACTTTTATATAGGTATAGATACTTTTATTCCAGTATGCTTCTCAAACAATTTG
* *
1810045 CACGCAAAATGCAT-TGATACACATATATAAAGTATCGATACTTCGAATTTCGAAACCTATTACT
66 CACGCAAAATGTATCT-ATACACATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACT
* * * * * * * * *
1810109 TTAAAGTGATAAGTTAATTAACAATGTAAACGATAAGAGTCTACTGATATATTGATAATAGGCAT
130 TTAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGT
1810174 AAATA
195 AAATA
* * * *
1810179 TCAAGTATCGACACTTTTATATAAGTAT-GTATAC-TTTATTCCAGTATGCTTTTCAAACAATTT
1 CCAAGTATCGATACTTTTATATAGGTATAG-ATACTTTTATTCCAGTATGCTTCTCAAACAATTT
* * **
1810242 GCACGCAAAATGTATCGATACACATATATAAAGTATCAATACTTATAATTTCGAAACCTATTACT
65 GCACGCAAAATGTATCTATACACATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACT
* * * * * *
1810307 TTAAAGTAATAGGTAAATTAACAATTTACACGGTAAACGTTTCTACCAGTATAATAAAAATAGGC
130 TTAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAG--TCTACCGGTATAATGATAATAGGC
*
1810372 GTAAATGT
193 GTAAAT-A
1810380 CCAAGTAT
1 CCAAGTAT
1810388 ATATTGATAC
Statistics
Matches: 707, Mismatches: 84, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
197 1 0.00
198 185 0.26
199 411 0.58
200 101 0.14
201 9 0.01
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (199 bp):
CCAAGTATCGATACTTTTATATAGGTATAGATACTTTTATTCCAGTATGCTTCTCAAACAATTTG
CACGCAAAATGTATCTATACACATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACTT
TAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGTA
AATA
Found at i:1811514 original size:111 final size:111
Alignment explanation
Indices: 1811299--1811520 Score: 365
Period size: 111 Copynumber: 2.0 Consensus size: 111
1811289 TGTTATATTG
1811299 TAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTGTACATG
1 TAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTGTACATG
* * *
1811364 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTT
66 TTATATTGTAAAATATCGATCATTTTTATAAAAGGATCGATACTTT
* * *
1811410 TAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTG
1 TAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTGTACATG
*
1811475 TTATATTGTAAAATATCGATACATTTTTAT-AAAGTATCGATACTTT
66 TTATATTGTAAAATATCGAT-CATTTTTATAAAAGGATCGATACTTT
1811521 ATAAGCGCTA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 95 0.92
112 8 0.08
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (111 bp):
TAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTGTACATG
TTATATTGTAAAATATCGATCATTTTTATAAAAGGATCGATACTTT
Found at i:1812152 original size:111 final size:111
Alignment explanation
Indices: 1811954--1812435 Score: 754
Period size: 111 Copynumber: 4.3 Consensus size: 111
1811944 AACTTTCAAA
* * ** *
1811954 AAAGTATCGATCATTTTTATAAAAAGTATATATACTTTCAACATATCAGGTAAATTTTACCGGTT
1 AAAGTATCTATCATTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
*
1812019 TTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
65 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
1812066 AAAGTATCTATGATTTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCGTTTT
1 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
1812131 TGTCATAATGAAACTGGTTTTG-CTATATTTTTACCTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTC-ATATTTTTACCTGTTATATTGT
*
1812177 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCTTTTT
1 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
*
1812242 TGTCATAATGAAACTGGTTTTGTCATATGTTTACCTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
1812288 AAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAATTTTACCGTTTT
1 AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
* *
1812353 TGTCATAATGAAACTGGTTTTGTCATATTTTTACTTGTTACATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
1812399 AAAATAT-TGATACATTTTTAT-AAAGTATCAATACTTT
1 AAAGTATCT-AT-CATTTTTATAAAAGGATCGATACTTT
1812436 ATAGCCGATA
Statistics
Matches: 344, Mismatches: 22, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
110 2 0.01
111 315 0.92
112 27 0.08
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (111 bp):
AAAGTATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:1813040 original size:111 final size:111
Alignment explanation
Indices: 1812868--1813572 Score: 1011
Period size: 111 Copynumber: 6.3 Consensus size: 111
1812858 AACTTTCAAA
* * * *
1812868 AAAGTATCA-ATCCTTTTTATAAAAAGTATCTATACTTTCAACATATTAAGTAAATTTTACCGGT
1 AAAGTAT-ATATCCTTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* * *
1812932 TTTGTTATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
64 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
1812980 AAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
1 AAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
* * * *
1813045 TGTCAAAATGACACTGGTTTTGTCACATTTTTACCTGTTTTATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * * * *
1813091 AAAGTATCTATCATTTTTATAAAAGGATCTATACTTTCAATATATTAGGTAAATTTTACCGTTTT
1 AAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
**
1813156 TGTCATAATGAAACTGGTTTTAACATATTTTTACCTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
*
1813202 AAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTT
1 AAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
* * *
1813267 TGTCAAAATGAAACTGGTTTTGTCACATTTTTACCTGTTTTATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * **
1813313 AAAGTATCTATCATTTTTATAAAAGGATTGATACTTTCAACATATCAGGTAAATTTTACCCTTTT
1 AAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
*
1813378 TGTCATAATGAAACTGGTTTTATCATATTTTTACCTGTTATATTGT
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
** *
1813424 AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGGTT
1 AAAGTATATATCCTTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
* *
1813489 TTTTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
1813536 AAAATATCA-ATACATTTTTAT-AAAGTATCGATACTTT
1 AAAGTAT-ATAT-CCTTTTTATAAAAGGATCGATACTTT
1813573 ATAGGCGCTA
Statistics
Matches: 535, Mismatches: 54, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
111 417 0.78
112 110 0.21
113 8 0.01
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (111 bp):
AAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:1813349 original size:914 final size:915
Alignment explanation
Indices: 1811300--1813349 Score: 3452
Period size: 914 Copynumber: 2.2 Consensus size: 915
1811290 GTTATATTGT
* * *
1811300 AACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTGTACATGT
1 AACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGT
*
1811365 TATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTTAACATATCAGGTAAATTTT
66 TATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTT
*
1811430 ACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGAT
131 ACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTAT
*
1811495 ACATTTTTATAAAGTATCGATACTTTATAAGCGCTATTACTGATTTTCCTTTAAATTCCAAAAGT
196 ACATTTTTATAAAGTATCGATACTTTATAAGCGATATTACTGATTTTCCTTTAAATTCCAAAAGT
*
1811560 GTCGATACTTATTTAAATGGAATCAATACTTTCAACATATCCGGTAGGTAGTTTAATATAATAGG
261 GTCGATACTTATTTAAATGGAATCAATACTTTCAACATATCCGATAGGTAGTTTAATATAATAGG
* * *
1811625 TAGGTATTTGACTGTGAAAATCATTAATTTAAGGTTATGTTTTGAGTGAGATTTAAGATATTAAT
326 TAGGTATTTCACTGTGAAAATCATTAAATAAAGGTTATGTTTTGAGTGAGATTTAAGATATTAAT
1811690 TTAGTAATTATACGCATCTAATGATTTATTTTTTATGTTACAGTATATATTATTATTAAATTAAA
391 TTAGTAATTATACGCATCTAATGATTTATTTTTTATGTTACAGTATATATTATTATTAAATTAAA
1811755 AACAATAAACATAAATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCC
456 AACAATAAACATAAATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCC
1811820 TAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAAT
521 TAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAAT
1811885 TAATATTGTAGATGGAAAACATAAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTT
586 TAATATTGTAGATGGAAAACATAAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTT
* *
1811950 CAAAAAAGTATCGATCATTTTTATAAAAAGTATATATACTTTCAACATATCAGGTAAATTTTACC
651 CAAAAAAGTATCAATCATTTTTATAAAAAGTATATATACTTTCAACATATCAAGTAAATTTTACC
* * *
1812015 GGTTTTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATGAT
716 GGTTTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGTAAAGTATATATCAT
* *
1812080 TTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCGTTTTTGTCATAATGAAAC
781 TTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCGGTTTTGTCAAAATGAAAC
*
1812145 TGGTTTTGCTATATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTTATAAAAGGATCGATA
846 TGGTTTTGCTACATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTTATAAAAGGATCGATA
1812210 CTTTC
911 CTTTC
* *
1812215 AACATATCAGGTAAATTTTACCTTTTTTGTCATAATGAAACTGGTTTTGTCATATGTTTACCTGT
1 AACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGT
*
1812280 TATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAATTTT
66 TATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTT
* *
1812345 ACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACTTGTTACATTGTAAAATAT-TGA
131 ACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCT-A
* *
1812409 TACATTTTTATAAAGTATCAATACTTTAT-AGCCGATATTACT-ACTTTTCTTTTAAATTCCAAA
195 TACATTTTTATAAAGTATCGATACTTTATAAG-CGATATTACTGA-TTTTCCTTTAAATTCCAAA
* * * * *
1812472 AGTTTCTATACTTATTTAAATGGAATCGATATTTTCAACATATCCGATAGGTAGTTTAATGTAAT
258 AGTGTCGATACTTATTTAAATGGAATCAATACTTTCAACATATCCGATAGGTAGTTTAATATAAT
*
1812537 AGGTTGGTATTTCACTGTGGAAAA-CATTAAATAAAGGTTATGTTTTGAGTGAGATTTAAGATAT
323 AGGTAGGTATTTCACTGT-GAAAATCATTAAATAAAGGTTATGTTTTGAGTGAGATTTAAGATAT
* *
1812601 TAATTTAGTAATTATACGCATCTAATTATTTATTTTTTATGTTACGGTATATATTATTATTAAAT
387 TAATTTAGTAATTATACGCATCTAATGATTTATTTTTTATGTTACAGTATATATTATTATTAAAT
*
1812666 TAAAAACAATAAACA-AAGATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAA
452 TAAAAACAATAAACATAA-ATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAA
*
1812730 ATT-CTAAATAATATTTTATAAAATATCAAAATAATCAAATAATTTTTTGTGTAAATGAAATTAT
516 ATTCCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTAT
* *
1812794 TAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTTT-AAACATAAATTACAT
581 TAAATTAATATTGTAGATGGAAAACATAAAACACTATT-AAAAAATTTTGAAACATAAATTACAT
* * *
1812858 AACTTTCAAAAAAGTATCAATCCTTTTTATAAAAAGTATCTATACTTTCAACATATTAAGTAAAT
645 AACTTTCAAAAAAGTATCAATCATTTTTATAAAAAGTATATATACTTTCAACATATCAAGTAAAT
*
1812923 TTTACCGGTTTTGTTATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGTAAAGTATA
710 TTTACCGGTTTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGTAAAGTATA
* *
1812988 TATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCAAAA
775 TATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCGGTTTTGTCAAAA
* *
1813053 TGACACTGGTTTTG-TCACATTTTTACCTGTTTTATTGTAAAGTATCTATCATTTTTATAAAAGG
840 TGAAACTGGTTTTGCT-ACATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTTATAAAAGG
*
1813117 ATCTATACTTTC
904 ATCGATACTTTC
* * **
1813129 AATATATTAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTAACATATTTTTACCTGT
1 AACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGT
*
1813194 TATATTGTAAAGTATATATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTT
66 TATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTT
* * * *
1813259 ACCGTTTTTGTCAAAATGAAACTGGTTTTGTCACATTTTTACCTGTTTTATTGTAAAGTATCTAT
131 ACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTAT
* *
1813324 -CATTTTTATAAAAGGATTGATACTTT
196 ACATTTTTAT-AAAGTATCGATACTTT
1813350 CAACATATCA
Statistics
Matches: 1063, Mismatches: 63, Indels: 19
0.93 0.06 0.02
Matches are distributed among these distances:
913 10 0.01
914 560 0.53
915 488 0.46
916 5 0.00
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (915 bp):
AACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGT
TATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTT
ACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTAT
ACATTTTTATAAAGTATCGATACTTTATAAGCGATATTACTGATTTTCCTTTAAATTCCAAAAGT
GTCGATACTTATTTAAATGGAATCAATACTTTCAACATATCCGATAGGTAGTTTAATATAATAGG
TAGGTATTTCACTGTGAAAATCATTAAATAAAGGTTATGTTTTGAGTGAGATTTAAGATATTAAT
TTAGTAATTATACGCATCTAATGATTTATTTTTTATGTTACAGTATATATTATTATTAAATTAAA
AACAATAAACATAAATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCC
TAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAAT
TAATATTGTAGATGGAAAACATAAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTT
CAAAAAAGTATCAATCATTTTTATAAAAAGTATATATACTTTCAACATATCAAGTAAATTTTACC
GGTTTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGTAAAGTATATATCAT
TTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCGGTTTTGTCAAAATGAAAC
TGGTTTTGCTACATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTTATAAAAGGATCGATA
CTTTC
Found at i:1813801 original size:34 final size:30
Alignment explanation
Indices: 1813762--1813830 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1813752 CGATATAACA
1813762 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1813796 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1813825 AATTTA
1 AATTTA
1813831 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1813841 original size:29 final size:30
Alignment explanation
Indices: 1813771--1813830 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1813761 AAATTTAAGG
1813771 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1813802 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1813831 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1813966 original size:21 final size:21
Alignment explanation
Indices: 1813910--1813967 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1813900 AGGGTGTCAA
*
1813910 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCATCCCTGC
1813931 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
1813952 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
1813968 TGCAATAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:1814074 original size:21 final size:21
Alignment explanation
Indices: 1814048--1814108 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
1814038 TGCATCCTTA
1814048 TGTGCATCGATGCATGAAGGT
1 TGTGCATCGATGCATGAAGGT
* *
1814069 TGTGCATCGATGCAT-CATGT
1 TGTGCATCGATGCATGAAGGT
* *
1814089 TGTGCATCCATGCACGAAGG
1 TGTGCATCGATGCATGAAGG
1814109 CTGCAACGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (21 bp):
TGTGCATCGATGCATGAAGGT
Found at i:1814074 original size:41 final size:41
Alignment explanation
Indices: 1814029--1814108 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
1814019 AATGCAATTA
* * *
1814029 GTGCATCGATGCATCCT-TATGTGCATCGATGCATGAAGGTT
1 GTGCATCGATGCATCATGT-TGTGCATCCATGCACGAAGGTT
1814070 GTGCATCGATGCATCATGTTGTGCATCCATGCACGAAGG
1 GTGCATCGATGCATCATGTTGTGCATCCATGCACGAAGG
1814109 CTGCAACGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCATGTTGTGCATCCATGCACGAAGGTT
Found at i:1814092 original size:20 final size:20
Alignment explanation
Indices: 1814029--1814102 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1814019 AATGCAATTA
*
1814029 GTGCATCGATGCATCCT-TAT
1 GTGCATCGATGCATCATGT-T
* *
1814049 GTGCATCGATGCATGAAGGTT
1 GTGCATCGATGCAT-CATGTT
1814070 GTGCATCGATGCATCATGTT
1 GTGCATCGATGCATCATGTT
*
1814090 GTGCATCCATGCA
1 GTGCATCGATGCA
1814103 CGAAGGCTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 30 0.65
21 15 0.33
22 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCATGTT
Found at i:1815348 original size:18 final size:19
Alignment explanation
Indices: 1815325--1815370 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
1815315 AATGATTTTC
*
1815325 TTTTGAAAACAAAAT-AGA
1 TTTTGAAAACAAAATGAAA
*
1815343 TTTTGAAAGCAAAATGAAA
1 TTTTGAAAACAAAATGAAA
1815362 TTTTGAAAA
1 TTTTGAAAA
1815371 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:1816671 original size:29 final size:30
Alignment explanation
Indices: 1816602--1816660 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1816592 AATTTAAGGA
*
1816602 AAAATGGTTTTTGTACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
1816633 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
1816661 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:1816769 original size:21 final size:21
Alignment explanation
Indices: 1816740--1816797 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1816730 AGGGTGTCAA
1816740 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1816761 AAG-GCATCCATGCATCCCTGC
1 -AGTGCATCCATGCACCCCTGC
1816782 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
1816798 TGCACTAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.22, C:0.40, G:0.19, T:0.19
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1816825 original size:42 final size:41
Alignment explanation
Indices: 1816740--1816833 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 41
1816730 AGGGTGTCAA
*
1816740 AGTGCATCCATGCACCCCTGCAAGGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGCAAGGCATCCATGCATCCATGC
*
1816782 AGTGCATCCATGCA-CCTGCACTAGTGCATCGATGCAT-CATGC
1 AGTGCATCCATGCACCCTGCA--AG-GCATCCATGCATCCATGC
1816824 AGTGCATCCA
1 AGTGCATCCA
1816834 CACACTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
40 6 0.13
42 30 0.64
43 11 0.23
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (41 bp):
AGTGCATCCATGCACCCTGCAAGGCATCCATGCATCCATGC
Found at i:1817073 original size:20 final size:22
Alignment explanation
Indices: 1817035--1817074 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1817025 TTTGAGTAGA
1817035 AAAATCATCCCCAAACGGCTTC
1 AAAATCATCCCCAAACGGCTTC
1817057 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1817075 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTTC
Found at i:1817690 original size:13 final size:13
Alignment explanation
Indices: 1817669--1817706 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1817659 AGTGCATCCA
*
1817669 TGCACCCCTGCAG
1 TGCATCCCTGCAG
1817682 TGCATCCCTGCAG
1 TGCATCCCTGCAG
*
1817695 TGCATCCATGCA
1 TGCATCCCTGCA
1817707 CCTGCACTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.21
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:1817720 original size:22 final size:19
Alignment explanation
Indices: 1817690--1817749 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
1817680 AGTGCATCCC
*
1817690 TGCAGTGCATCCATGCACC
1 TGCAGTGCATCCATGCACA
*
1817709 TGCACTAGTGCATCGATGCATCA
1 TG--C-AGTGCATCCATGCA-CA
1817732 TGCAGTGCATCCATGCAC
1 TGCAGTGCATCCATGCAC
1817750 TCAAACACCG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 3 0.09
20 13 0.38
21 2 0.06
22 13 0.38
23 3 0.09
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (19 bp):
TGCAGTGCATCCATGCACA
Found at i:1817748 original size:13 final size:13
Alignment explanation
Indices: 1817677--1817748 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 13
1817667 CATGCACCCC
*
1817677 TGCAGTGCATCCC
1 TGCAGTGCATCCA
1817690 TGCAGTGCATCCA
1 TGCAGTGCATCCA
* *
1817703 TGCACCTGCA-CTA
1 TGCA-GTGCATCCA
1817716 GTGCATCGATGCAT-CA
1 -TGCA--G-TGCATCCA
1817732 TGCAGTGCATCCA
1 TGCAGTGCATCCA
1817745 TGCA
1 TGCA
1817749 CTCAAACACC
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
12 5 0.10
13 25 0.52
14 8 0.17
15 5 0.10
16 5 0.10
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (13 bp):
TGCAGTGCATCCA
Found at i:1817795 original size:20 final size:20
Alignment explanation
Indices: 1817770--1817843 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1817760 AATGCAATTA
1817770 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTTAT
***
1817790 GTGCATCGATGCATCAAGGAT
1 GTGCATCGATGCATC-CTTAT
1817811 GTGCATCGATGCATCCTGT-T
1 GTGCATCGATGCATCCT-TAT
*
1817831 GTGCATCCATGCA
1 GTGCATCGATGCA
1817844 CGAAGGCTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTAT
Done.