Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 49 of 51
Found at i:12134943 original size:21 final size:21
Alignment explanation
Indices: 12134914--12134953 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12134904 TCGTGGCGGC
* *
12134914 AAAAGATGTAGAAGTAAAAGG
1 AAAAAATGTAGAAGAAAAAGG
*
12134935 AAAAAATGTTGAAGAAAAA
1 AAAAAATGTAGAAGAAAAA
12134954 AGGTTGAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (21 bp):
AAAAAATGTAGAAGAAAAAGG
Found at i:12134966 original size:15 final size:15
Alignment explanation
Indices: 12134931--12134969 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
12134921 GTAGAAGTAA
*
12134931 AAGGAAAAAATGTTG
1 AAGGAAAAAAGGTTG
12134946 AA-GAAAAAAGGTTG
1 AAGGAAAAAAGGTTG
12134960 AAGGAAAAAA
1 AAGGAAAAAA
12134970 AGACAAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (15 bp):
AAGGAAAAAAGGTTG
Found at i:12150251 original size:15 final size:16
Alignment explanation
Indices: 12150231--12150260 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12150221 ATGGTGTATT
12150231 TTGAAC-CGATTTAGA
1 TTGAACACGATTTAGA
12150246 TTGAACACGATTTAG
1 TTGAACACGATTTAG
12150261 TGTGAAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (16 bp):
TTGAACACGATTTAGA
Found at i:12155243 original size:45 final size:45
Alignment explanation
Indices: 12155176--12155261 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
12155166 CTCTCAACTT
* * *
12155176 CTTCTTAATATCTTGAATAAAAGGATAGAGCTTTATTTACCATCA
1 CTTCTTAATATCTTGAACAAAAGGATAGAACATTATTTACCATCA
12155221 CTTCTTAATATCTTGAACAAAAGGATAGAACATTATTTACC
1 CTTCTTAATATCTTGAACAAAAGGATAGAACATTATTTACC
12155262 TTCCTAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (45 bp):
CTTCTTAATATCTTGAACAAAAGGATAGAACATTATTTACCATCA
Found at i:12156434 original size:23 final size:23
Alignment explanation
Indices: 12156370--12156441 Score: 117
Period size: 23 Copynumber: 3.1 Consensus size: 23
12156360 TGTTGATAAC
**
12156370 AATTCTATTTCTTATTTAAAAGA
1 AATTCTATTTCTTATTTAGGAGA
12156393 AATTCTATTTCTTATTTAGGAGA
1 AATTCTATTTCTTATTTAGGAGA
*
12156416 AATTCTATTTCTTAGTTAGGAGA
1 AATTCTATTTCTTATTTAGGAGA
12156439 AAT
1 AAT
12156442 AAAAAATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (23 bp):
AATTCTATTTCTTATTTAGGAGA
Found at i:12159559 original size:23 final size:23
Alignment explanation
Indices: 12159532--12159575 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12159522 AAGAAAAAAA
*
12159532 TTTGAAATCCCTTTTAGAAAGAT
1 TTTGAAACCCCTTTTAGAAAGAT
*
12159555 TTTGACACCCCTTTTAGAAAG
1 TTTGAAACCCCTTTTAGAAAG
12159576 GCTTTGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (23 bp):
TTTGAAACCCCTTTTAGAAAGAT
Found at i:12160035 original size:64 final size:64
Alignment explanation
Indices: 12159920--12160047 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 64
12159910 TAAATCTTCA
* *
12159920 ATTTTGATTTTTGAAATCTTAAAGTCATTTCTCAAACTTCATTCTATTTTTCAAAATCAAATTT
1 ATTTTGATTTTTAAAATCTCAAAGTCATTTCTCAAACTTCATTCTATTTTTCAAAATCAAATTT
* *
12159984 ATTTTGATTTTTAAAATCTCAAAGTCATTTTTCAAAACTTCATT-T-TGTTTTCAAAATCCAATT
1 ATTTTGATTTTTAAAATCTCAAAGTCATTTCTC-AAACTTCATTCTAT-TTTTCAAAATCAAATT
12160047 T
64 T
12160048 TGCTTTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
63 1 0.02
64 47 0.81
65 10 0.17
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (64 bp):
ATTTTGATTTTTAAAATCTCAAAGTCATTTCTCAAACTTCATTCTATTTTTCAAAATCAAATTT
Found at i:12160047 original size:19 final size:19
Alignment explanation
Indices: 12160012--12160049 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12160002 TCAAAGTCAT
*
12160012 TTTTCAAAACTTCATTTTG
1 TTTTCAAAACTCCATTTTG
12160031 TTTTCAAAA-TCCAATTTTG
1 TTTTCAAAACTCC-ATTTTG
12160050 CTTTAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTTCAAAACTCCATTTTG
Found at i:12163578 original size:18 final size:18
Alignment explanation
Indices: 12163557--12163591 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12163547 TCCTTTTAAG
*
12163557 TTTTAGATTTTTTTTTCT
1 TTTTAGAATTTTTTTTCT
*
12163575 TTTTATAATTTTTTTTC
1 TTTTAGAATTTTTTTTC
12163592 GATGATTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTAGAATTTTTTTTCT
Found at i:12165074 original size:14 final size:14
Alignment explanation
Indices: 12165055--12165081 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12165045 GAATTTTTCG
12165055 GTCAAAGTCAACGA
1 GTCAAAGTCAACGA
12165069 GTCAAAGTCAACG
1 GTCAAAGTCAACG
12165082 CGTTGACTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (14 bp):
GTCAAAGTCAACGA
Found at i:12172143 original size:14 final size:14
Alignment explanation
Indices: 12172111--12172150 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12172101 TTGACTTTTT
*
12172111 GGTCAAAGTTAA-C
1 GGTCAAAGTCAATC
*
12172124 GGTCAAAGTCAATG
1 GGTCAAAGTCAATC
12172138 GGTCAAAGTCAAT
1 GGTCAAAGTCAAT
12172151 AGGTTGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (14 bp):
GGTCAAAGTCAATC
Found at i:12174233 original size:16 final size:16
Alignment explanation
Indices: 12174212--12174251 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
12174202 AACAGGGCAG
12174212 CAGATTCTGCTCAAAA
1 CAGATTCTGCTCAAAA
*
12174228 CAGATTATGCTCAAAA
1 CAGATTCTGCTCAAAA
12174244 CAGATTCT
1 CAGATTCT
12174252 ATCGGCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (16 bp):
CAGATTCTGCTCAAAA
Found at i:12176171 original size:15 final size:14
Alignment explanation
Indices: 12176142--12176191 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
12176132 ATACGGGTTA
12176142 TGACTC-GGACGAGT
1 TGACTCAGG-CGAGT
*
12176156 TGACTCAGTTCGAGT
1 TGACTCAG-GCGAGT
12176171 TGACTCAGGCGAGT
1 TGACTCAGGCGAGT
12176185 TGACTCA
1 TGACTCA
12176192 ATTCAGACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (14 bp):
TGACTCAGGCGAGT
Found at i:12179050 original size:21 final size:21
Alignment explanation
Indices: 12179025--12179064 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12179015 AAGACTTTAT
12179025 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
12179046 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
12179065 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:12182942 original size:21 final size:22
Alignment explanation
Indices: 12182894--12182994 Score: 75
Period size: 23 Copynumber: 4.6 Consensus size: 22
12182884 ACACTAGACA
* *
12182894 GTGCATCGATATATCCTTTGAAT
1 GTGCATCGATACA-CCATTGAAT
* *
12182917 ATGCATCGATACACC-TTGAAG
1 GTGCATCGATACACCATTGAAT
* *
12182938 GTGCACCGATGCACTCATTGAAT
1 GTGCATCGATACAC-CATTGAAT
* *
12182961 GTGCATCGATGCA-C-TCTG-TT
1 GTGCATCGATACACCAT-TGAAT
12182981 GTGCATCGATACAC
1 GTGCATCGATACAC
12182995 TCGTCGGGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
20 14 0.22
21 19 0.30
22 3 0.05
23 28 0.44
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (22 bp):
GTGCATCGATACACCATTGAAT
Found at i:12182964 original size:23 final size:22
Alignment explanation
Indices: 12182911--12182996 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 22
12182901 GATATATCCT
* *
12182911 TTGAATATGCATCGATACAC-C
1 TTGAATGTGCATCGATGCACTC
* *
12182932 TTGAAGGTGCACCGATGCACTC
1 TTGAATGTGCATCGATGCACTC
12182954 ATTGAATGTGCATCGATGCACTC
1 -TTGAATGTGCATCGATGCACTC
* *
12182977 -TG-TTGTGCATCGATACACTC
1 TTGAATGTGCATCGATGCACTC
12182997 GTCGGGTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
20 16 0.29
21 18 0.33
22 1 0.02
23 20 0.36
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
TTGAATGTGCATCGATGCACTC
Found at i:12187778 original size:9 final size:8
Alignment explanation
Indices: 12187744--12187823 Score: 54
Period size: 9 Copynumber: 9.2 Consensus size: 8
12187734 AAGGAAAAAT
12187744 AAAATAAA
1 AAAATAAA
12187752 AAACATAAAA
1 AAA-AT-AAA
12187762 AAAGATAAA
1 AAA-ATAAA
12187771 CAAAATAAA
1 -AAAATAAA
*
12187780 GAAATAAA
1 AAAATAAA
* *
12187788 TCAAA-GAA
1 -AAAATAAA
12187796 AAAATAAA
1 AAAATAAA
*
12187804 AATATTAAA
1 AA-AATAAA
12187813 TAAAATAAA
1 -AAAATAAA
12187822 AA
1 AA
12187824 TATTAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
7 3 0.05
8 18 0.32
9 23 0.40
10 13 0.23
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (8 bp):
AAAATAAA
Found at i:12187793 original size:28 final size:28
Alignment explanation
Indices: 12187724--12187798 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
12187714 AATAAATGTT
* *
12187724 AAATAAATCCAAGGAAAAATAAAATAAAA
1 AAATAAAT-CAAAGAAAAACAAAATAAAA
* * *
12187753 AACATAAA-AAAAGATAAACAAAATAAAG
1 AA-ATAAATCAAAGAAAAACAAAATAAAA
12187781 AAATAAATCAAAGAAAAA
1 AAATAAATCAAAGAAAAA
12187799 ATAAAAATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.14
28 25 0.68
29 2 0.05
30 5 0.14
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.12
Consensus pattern (28 bp):
AAATAAATCAAAGAAAAACAAAATAAAA
Found at i:12187840 original size:18 final size:18
Alignment explanation
Indices: 12187796--12187834 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12187786 AATCAAAGAA
12187796 AAAATAAAAATATTAAAT
1 AAAATAAAAATATTAAAT
12187814 AAAATAAAAATATTAAAT
1 AAAATAAAAATATTAAAT
12187832 AAA
1 AAA
12187835 TGAAAAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAAAATATTAAAT
Found at i:12187862 original size:6 final size:7
Alignment explanation
Indices: 12187738--12187944 Score: 71
Period size: 7 Copynumber: 27.4 Consensus size: 7
12187728 AAATCCAAGG
12187738 AAAAATA
1 AAAAATA
12187745 AAATAA-A
1 AAA-AATA
*
12187752 AAACATA
1 AAAAATA
12187759 AAAAA-A
1 AAAAATA
* *
12187765 GATAA-A
1 AAAAATA
*
12187771 CAAAATA
1 AAAAATA
12187778 AAGAAATA
1 AA-AAATA
*
12187786 AATCAAAGA
1 AA--AAATA
12187795 AAAAATA
1 AAAAATA
12187802 AAAATATTAA
1 AAAA-A-T-A
12187812 ATAAAATA
1 A-AAAATA
12187820 AAAATATTA
1 AAAA-A-TA
12187829 AATAAATGA
1 AA-AAAT-A
**
12187838 AAAGGGTA
1 AAA-AATA
*
12187846 TAAAATA
1 AAAAATA
12187853 AAAAATA
1 AAAAATA
*
12187860 AAAAATTTT
1 AAAAA--TA
** *
12187869 AAATTTT
1 AAAAATA
*
12187876 AAAAGTA
1 AAAAATA
12187883 ATAAAATA
1 A-AAAATA
12187891 AAAAATA
1 AAAAATA
* *
12187898 AGAAGTA
1 AAAAATA
12187905 AAAACATA
1 AAAA-ATA
12187913 AAACAA-A
1 AAA-AATA
*
12187920 TAATAATA
1 -AAAAATA
12187928 AAAAATA
1 AAAAATA
12187935 AAAAATA
1 AAAAATA
12187942 AAA
1 AAA
12187945 TAAAATTAAA
Statistics
Matches: 150, Mismatches: 29, Indels: 42
0.68 0.13 0.19
Matches are distributed among these distances:
6 9 0.06
7 78 0.52
8 33 0.22
9 22 0.15
10 5 0.03
11 3 0.02
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (7 bp):
AAAAATA
Found at i:12187913 original size:22 final size:19
Alignment explanation
Indices: 12187875--12187969 Score: 95
Period size: 17 Copynumber: 4.7 Consensus size: 19
12187865 TTTTAAATTT
12187875 TAAAAGTAATAAAATAAAAAA
1 TAAAA-TAA-AAAATAAAAAA
12187896 TAAGAAGTAAAAACATAAAACAAA
1 TAA-AA-TAAAAA-AT-AAA-AAA
12187920 TAATAATAAAAAATAAAAAA
1 TAA-AATAAAAAATAAAAAA
*
12187940 TAAAAT--AAAATTAAAAA
1 TAAAATAAAAAATAAAAAA
12187957 TAAAATAAAAAAT
1 TAAAATAAAAAAT
12187970 GATAAAATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
17 16 0.24
19 8 0.12
20 6 0.09
21 9 0.14
22 10 0.15
23 9 0.14
24 8 0.12
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (19 bp):
TAAAATAAAAAATAAAAAA
Found at i:12187939 original size:24 final size:23
Alignment explanation
Indices: 12187882--12187969 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 23
12187872 TTTTAAAAGT
12187882 AATAAAATAAAAAATAAGAAGTAAAA
1 AATAAAA-AAAAAATAA-AA-TAAAA
*
12187908 ACAT--AAAACAAATAATAATAAAA
1 A-ATAAAAAAAAAATAA-AATAAAA
*
12187931 AATAAAAAATAAAATAAAATTAAA
1 AATAAAAAA-AAAATAAAATAAAA
12187955 AATAAAATAAAAAAT
1 AATAAAA-AAAAAAT
12187970 GATAAAATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
22 2 0.04
23 6 0.11
24 32 0.60
25 10 0.19
26 1 0.02
27 2 0.04
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (23 bp):
AATAAAAAAAAAATAAAATAAAA
Found at i:12187981 original size:21 final size:21
Alignment explanation
Indices: 12187951--12187993 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12187941 AAAATAAAAT
*
12187951 TAAAAATAAAATAAAAAATGA
1 TAAAAATAAAAGAAAAAATGA
* *
12187972 TAAAATTAAAAGGAAAAATGA
1 TAAAAATAAAAGAAAAAATGA
12187993 T
1 T
12187994 TAACTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAAAATAAAAGAAAAAATGA
Found at i:12189027 original size:20 final size:20
Alignment explanation
Indices: 12188987--12189027 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12188977 AATACTATAT
* *
12188987 TATATGAATAGTATCGGTAC
1 TATATGAATAGTACCGATAC
12189007 TATATGAATAGTACCGATAC
1 TATATGAATAGTACCGATAC
12189027 T
1 T
12189028 GTGCGAACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (20 bp):
TATATGAATAGTACCGATAC
Found at i:12192171 original size:18 final size:19
Alignment explanation
Indices: 12192148--12192184 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12192138 CAACAATTGG
*
12192148 TAACAATTAGTAT-CTTTT
1 TAACAATTAATATCCTTTT
12192166 TAACAATTAATATCCTTTT
1 TAACAATTAATATCCTTTT
12192185 GTTAATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.49
Consensus pattern (19 bp):
TAACAATTAATATCCTTTT
Found at i:12193031 original size:23 final size:23
Alignment explanation
Indices: 12193001--12193049 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12192991 TGGTGGTTGG
*
12193001 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
12193024 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
12193047 TTT
1 TTT
12193050 GGTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:12194203 original size:22 final size:20
Alignment explanation
Indices: 12194155--12194193 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12194145 TATTCCATAA
*
12194155 TGCTACAGGGGTATCGATAC
1 TGCTACACGGGTATCGATAC
12194175 TGCTACACGGGTATCGATA
1 TGCTACACGGGTATCGATA
12194194 ATGTGCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
TGCTACACGGGTATCGATAC
Found at i:12195712 original size:12 final size:12
Alignment explanation
Indices: 12195695--12195778 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 12
12195685 ACAACAAAGG
12195695 AAATAATAAATA
1 AAATAATAAATA
12195707 AAATAAATAAA-A
1 AAAT-AATAAATA
12195719 AAATATATATTAATA
1 AAATA-ATA--AATA
* *
12195734 AAATAGTGAAT-
1 AAATAATAAATA
12195745 AAATAATATTAATA
1 AAATAATA--AATA
*
12195759 TAAT-ATATAATA
1 AAATAATA-AATA
12195771 AAA-AATAA
1 AAATAATAA
12195779 TTTTTTAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 8 0.14
12 25 0.44
13 12 0.21
14 6 0.11
15 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
AAATAATAAATA
Found at i:12195734 original size:27 final size:26
Alignment explanation
Indices: 12195695--12195779 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 26
12195685 ACAACAAAGG
12195695 AAATAATA--AATAAAATAAATAAAA
1 AAATAATATTAATAAAATAAATAAAA
* * *
12195719 AAATATATATTAATAAAAT-AGTGAAT
1 AAATA-ATATTAATAAAATAAATAAAA
12195745 AAATAATATTAATATAATATATAAT-AAA
1 AAATAATATTAATA-AA-ATA-AATAAAA
12195773 AAATAAT
1 AAATAAT
12195780 TTTTTAAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
24 5 0.10
25 12 0.24
26 11 0.22
27 10 0.20
28 9 0.18
29 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (26 bp):
AAATAATATTAATAAAATAAATAAAA
Found at i:12195913 original size:36 final size:36
Alignment explanation
Indices: 12195816--12196011 Score: 177
Period size: 38 Copynumber: 5.3 Consensus size: 36
12195806 GCTTTTTAAA
* *
12195816 AAAAATTATTTTCAAAA-TCATATAATATAATATATTTTC
1 AAAAA-TATTTTCAAAACT-ATATTATAT-ATAT-TTTTT
*
12195855 AAAAATATTTT-AAAATTATATATTATATATATTTTTT
1 AAAAATATTTTCAAAA--CTATATTATATATATTTTTT
* *
12195892 AAAAATATTTTCAAAACTATA-TATTATATAATTTTC
1 AAAAATATTTTCAAAACTATATTA-TATATATTTTTT
* *
12195928 AAAAATGTTTT-AAAACTATA-TATTATATATATTTT
1 AAAAATATTTTCAAAACTATATTA-TATATATTTTTT
*
12195963 CAAAATATTTTCAAAACTATATATTATATATATTTTTT
1 AAAAATATTTTCAAAAC--TATATTATATATATTTTTT
* *
12196001 CAAAATGTTTT
1 AAAAATATTTT
12196012 TTAAAAACCA
Statistics
Matches: 135, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
35 32 0.24
36 29 0.21
37 19 0.14
38 39 0.29
39 15 0.11
40 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (36 bp):
AAAAATATTTTCAAAACTATATTATATATATTTTTT
Found at i:12196144 original size:37 final size:37
Alignment explanation
Indices: 12195835--12196146 Score: 306
Period size: 35 Copynumber: 8.4 Consensus size: 37
12195825 TTTCAAAATC
* * *
12195835 ATATAATATAATATATTTTCAAAAAT-ATTTT-AAAATT
1 ATATATTAT-ATATATTTTC-AAAATGTTTTTAAAAACT
* * *
12195872 ATATATTATATATATTTTTTAAAAAT-ATTTTCAAAACT
1 ATATATTATATATA--TTTTCAAAATGTTTTTAAAAACT
12195910 ATATATTATATA-ATTTTCAAAAATG-TTTT-AAAACT
1 ATATATTATATATATTTTC-AAAATGTTTTTAAAAACT
* *
12195945 ATATATTATATATATTTTCAAAAT-ATTTTCAAAACT
1 ATATATTATATATATTTTCAAAATGTTTTTAAAAACT
*
12195981 ATATATTATATATATTTTTTCAAAATGTTTTTTAAAAACC
1 ATATATTATATATA--TTTTCAAAATG-TTTTTAAAAACT
12196021 ATATATTATATA-AGTTTTCAAAATGTTTGTTTAAAAAAC-
1 ATATATTATATATA-TTTTCAAAATG-TT-TTT-AAAAACT
* * *
12196060 ATATATTATATA-AGTTTTCAACATGTTTTCAAAAATT
1 ATATATTATATATA-TTTTCAAAATGTTTTTAAAAACT
*
12196097 ATATA-T-TATATATTTTCAAAATGTTTTTAAAAACC
1 ATATATTATATATATTTTCAAAATGTTTTTAAAAACT
12196132 ATATATTATATATAT
1 ATATATTATATATAT
12196147 ATCAAAAAGA
Statistics
Matches: 242, Mismatches: 15, Indels: 36
0.83 0.05 0.12
Matches are distributed among these distances:
35 59 0.24
36 48 0.20
37 33 0.14
38 47 0.19
39 28 0.12
40 27 0.11
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAAATGTTTTTAAAAACT
Found at i:12196166 original size:37 final size:35
Alignment explanation
Indices: 12196014--12196166 Score: 92
Period size: 35 Copynumber: 4.1 Consensus size: 35
12196004 AATGTTTTTT
* * *
12196014 AAAAACCATATATTATATAAGTTTTCAAAATGTTTGTTTA
1 AAAAACCATATATTATAT-A-TTATCAAAAAG--T-TTAA
* * * **
12196054 AAAAA-CATATATTATATAAGTTTTCAACATGTTTTC
1 AAAAACCATATATTATAT-A-TTATCAAAAAGTTTAA
** * * **
12196090 AAAAATTATATATTATATATTTTCAAAATGTTTTT
1 AAAAACCATATATTATATATTATCAAAAAGTTTAA
12196125 AAAAACCATATATTATATATATATCAAAAAGATTTAA
1 AAAAACCATATATTATATAT-TATCAAAAAG-TTTAA
12196162 AAAAA
1 AAAAA
12196167 ATTATACGAT
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
35 32 0.32
36 17 0.17
37 20 0.20
39 25 0.25
40 5 0.05
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (35 bp):
AAAAACCATATATTATATATTATCAAAAAGTTTAA
Found at i:12203933 original size:43 final size:42
Alignment explanation
Indices: 12203811--12204592 Score: 445
Period size: 43 Copynumber: 18.3 Consensus size: 42
12203801 TTTTTATAAC
* **
12203811 GCCCCTAATTTTTCAATCAT-ACTTTTTATTTTTATAATTGAG
1 GCCCCTAATTTTTTAATC-TCACTTTTTACCTTTATAATTGAG
**** * * *
12203853 GTATTTAATTTTTTTAATTTTA-TTTTT--CTGTATAATTGAG
1 GCCCCTAA-TTTTTTAATCTCACTTTTTACCTTTATAATTGAG
*
12203893 GCCCCTAATTTTTGTAATC-CTACTTTTTATCTTTATAATTGAG
1 GCCCCTAATTTTT-TAATCTC-ACTTTTTACCTTTATAATTGAG
* * * * * *
12203936 TCTCTTAATTTTTGTAATCCCACTTTTTACATTTATAATTAAG
1 GCCCCTAATTTTT-TAATCTCACTTTTTACCTTTATAATTGAG
* * * * *
12203979 GCCCCTAATTTTTGCAGTCCCACTTTTTACGTTTATAATTAAG
1 GCCCCTAATTTTT-TAATCTCACTTTTTACCTTTATAATTGAG
* * ** * *
12204022 GCCCTTAATTTTTTTTTCAATTTCACTTGCTA-GTTTAATAATTGAA
1 GCCCCTAA---TTTTTT-AATCTCACTTTTTACCTTT-ATAATTGAG
* * * * *
12204068 ACCCCTAATTTTTTTAT-TCTAGCTTTTTACTTTTTTAATTGAT
1 GCCCCTAATTTTTTAATCTC-A-CTTTTTACCTTTATAATTGAG
* * **
12204111 GCTCCTAATTTTTTCAATCTAACTTTTTAAATTTATAATTGAG
1 GCCCCTAATTTTTT-AATCTCACTTTTTACCTTTATAATTGAG
* * * * * *
12204154 GCTCCT-ATTTTTTCAATATCACTTTCTAGCTTTATAGTTGAA
1 GCCCCTAATTTTTT-AATCTCACTTTTTACCTTTATAATTGAG
* * * * * * *
12204196 GCCCTTAATTTTTTAATCACATTTTTTTTTCATTTATAACTAAG
1 GCCCCTAATTTTTTAATCTCA--CTTTTTACCTTTATAATTGAG
* * * * *
12204240 ACTCCTAATTTTTTTCAATATCA--TTTTACCTTCATAATTGAA
1 GCCCCTAA-TTTTTT-AATCTCACTTTTTACCTTTATAATTGAG
* * *
12204282 GCCCCTAATTTTTTCAGTCTCACTTTTTTACCTTTATAATTAAA
1 GCCCCTAATTTTTT-AATCTCAC-TTTTTACCTTTATAATTGAG
* * *
12204326 GTCCATAATTTTTTAATCTCAC-TTTTACCTTTATAATTGAT
1 GCCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAG
* * * *
12204367 GCTCCTAATTTTTTCAATATCACTTTTTACCTTTATAGTTGAA
1 GCCCCTAATTTTTT-AATCTCACTTTTTACCTTTATAATTGAG
* * * * *
12204410 GCACATAATTTTTTAATCTAATTTTTTACCTTTATAATTTAG
1 GCCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAG
* * *** *
12204452 GTCTCTAATTTTTTTCAATCTCACTTCCCACCTTTTATAATTGAA
1 GCCCCTAA-TTTTTT-AATCTCACTTTTTACC-TTTATAATTGAG
** * *
12204497 G-TGCTAATTTTTTAATCTCGCTTTTTACTTTTATAATTGAG
1 GCCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAG
* * * * * *
12204538 ACCCCTAATTTTTCCAATGTAACTTTTTTACTTTTATAATTTAG
1 GCCCCTAATTTTT-TAATCTCAC-TTTTTACCTTTATAATTGAG
* *
12204582 GACGCTAATTT
1 GCCCCTAATTT
12204593 AATAATTTTT
Statistics
Matches: 568, Mismatches: 138, Indels: 66
0.74 0.18 0.09
Matches are distributed among these distances:
39 5 0.01
40 20 0.04
41 58 0.10
42 123 0.22
43 213 0.38
44 95 0.17
45 22 0.04
46 32 0.06
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (42 bp):
GCCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAG
Found at i:12204079 original size:132 final size:128
Alignment explanation
Indices: 12203923--12204384 Score: 303
Period size: 132 Copynumber: 3.6 Consensus size: 128
12203913 TACTTTTTAT
** * * *
12203923 CTTTATAATTGAGTCTCTTAATTTTTGTAATCCCA-CTTTTTACATTTATAATTAAGGCCCCTAA
1 CTTTATAATTGAAACCCCTAATTTTT-TAATCCCATCTTTTTACATTTATAATTAAGGCTCCTAA
* * ** *
12203987 TTTTTGCAGTCCCACTTTTTACGTTTATAATTAAGGC-CCTTAATTTTTTTTTCAATTTCACTTG
65 TTTTTGCAATCCAACTTTTTAAATTTATAATTAAGGCTCC-T-A---TTTTTTCAATATCACTTG
12204051 CTAG
125 CTAG
* * * * * * * *
12204055 -TTTAATAATTGAAACCCCTAATTTTTTTATTCTAGCTTTTTACTTTTTTAATTGATGCTCCTAA
1 CTTT-ATAATTGAAACCCCTAATTTTTTAATCCCATCTTTTTACATTTATAATTAAGGCTCCTAA
* * * *
12204119 TTTTTTCAATCTAACTTTTTAAATTTATAATTGAGGCTCCTATTTTTTCAATATCACTTTCTAG
65 TTTTTGCAATCCAACTTTTTAAATTTATAATTAAGGCTCCTATTTTTTCAATATCACTTGCTAG
* * * * * * * *
12204183 CTTTATAGTTGAAGCCCTTAATTTTTTAATCACATTTTTTTTTCATTTATAACTAAGACTCCTAA
1 CTTTATAATTGAAACCCCTAATTTTTTAATCCCA-TCTTTTTACATTTATAATTAAGGCTCCTAA
* * * ** * * * * **
12204248 TTTTTTTCAAT--ATCATTTTACCTTCATAATTGAA-GCCCCTAATTTTTTCAGTCTCACTTTTT
65 -TTTTTGCAATCCAACTTTTTAAATTTATAATT-AAGGCTCCT-ATTTTTTCAATATCAC-TTGC
*
12204310 TAC
126 TAG
* * * * * *
12204313 CTTTATAATT-AAAGTCCATAATTTTTTAATCTCA-C-TTTTACCTTTATAATTGATGCTCCTAA
1 CTTTATAATTGAAA-CCCCTAATTTTTTAATCCCATCTTTTTACATTTATAATTAAGGCTCCTAA
*
12204375 TTTTTTCAAT
65 TTTTTGCAAT
12204385 ATCACTTTTT
Statistics
Matches: 260, Mismatches: 60, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
126 10 0.04
127 21 0.08
128 63 0.24
129 41 0.16
130 41 0.16
131 9 0.03
132 73 0.28
133 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (128 bp):
CTTTATAATTGAAACCCCTAATTTTTTAATCCCATCTTTTTACATTTATAATTAAGGCTCCTAAT
TTTTGCAATCCAACTTTTTAAATTTATAATTAAGGCTCCTATTTTTTCAATATCACTTGCTAG
Found at i:12204109 original size:175 final size:174
Alignment explanation
Indices: 12203884--12204209 Score: 394
Period size: 175 Copynumber: 1.9 Consensus size: 174
12203874 ATTTTTCTGT
** *
12203884 ATAATTGAGGCCCCTAATTTTTGTAATCCTACTTTTTATCTTTATAATTGA-GTCTCTTAATTTT
1 ATAATTGAAACCCCTAATTTTTGTAATCCTACTTTTTATCTTTATAATTGATG-CTCCTAATTTT
* * * * *
12203948 TGT-AATCCCACTTTTTACATTTATAATTAAGGCCCCTAATTTTTGCAGTCCCACTTTTTA-CGT
65 T-TCAATCCAACTTTTTAAATTTATAATTAAGGCCCCT-ATTTTTGCAATACCACTTTCTAGC-T
12204011 TTATAATT-AAGGCCCTTAATTTTTTTTTCAATTTCACTTGCTAGTTTA
127 TTATAATTGAA-GCCCTTAATTTTTTTTTCAATTTCACTTGCTAGTTTA
* * *
12204059 ATAATTGAAACCCCTAATTTTT-TTATTCTAGCTTTTTA-CTTTTTTAATTGATGCTCCTAATTT
1 ATAATTGAAACCCCTAATTTTTGTAATCCTA-CTTTTTATC-TTTATAATTGATGCTCCTAATTT
* * * * *
12204122 TTTCAATCTAACTTTTTAAATTTATAATTGAGGCTCCTATTTTTTCAATATCACTTTCTAGCTTT
64 TTTCAATCCAACTTTTTAAATTTATAATTAAGGCCCCTATTTTTGCAATACCACTTTCTAGCTTT
*
12204187 ATAGTTGAAGCCCTTAATTTTTT
129 ATAATTGAAGCCCTTAATTTTTT
12204210 AATCACATTT
Statistics
Matches: 128, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
174 47 0.37
175 80 0.62
176 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (174 bp):
ATAATTGAAACCCCTAATTTTTGTAATCCTACTTTTTATCTTTATAATTGATGCTCCTAATTTTT
TCAATCCAACTTTTTAAATTTATAATTAAGGCCCCTATTTTTGCAATACCACTTTCTAGCTTTAT
AATTGAAGCCCTTAATTTTTTTTTCAATTTCACTTGCTAGTTTA
Found at i:12204397 original size:128 final size:127
Alignment explanation
Indices: 12203883--12204578 Score: 490
Period size: 128 Copynumber: 5.4 Consensus size: 127
12203873 TATTTTTCTG
* * *
12203883 TATAATTGAGGCCCCTAATTTTTGT-AATC-CTACTTTTTATCTTTATAATT-GAGTCTCTTAAT
1 TATAATTGAAGCCCCTAATTTTT-TCAATCTC-ACTTTTTACCTTTATAATTAAAGTC-CTTAAT
* * * * *
12203945 TTTTGTAATCCCACTTTTTACATTTATAATT-AAGGCCCCTAATTTTTGCAGTCCCACTTTTTAC
63 TTTT-TAATCTCAC-TTTTACATTTATAATTGAA-GCTCCTAATTTTTTCAATCTCACTTTTTAC
*
12204009 GTT
125 CTT
* * ** * * *
12204012 TATAATT-AAGGCCCTTAATTTTTTTTTCAATTTCACTTGCTA-GTTTAATAATTGAAA-CCCCT
1 TATAATTGAA-GCCCCTAA---TTTTTTCAATCTCACTTTTTACCTTT-ATAATT-AAAGTCCTT
* * * * *
12204074 AATTTTTTTAT-TCTAGCTTTTTACTTTTTTAATTGATGCTCCTAATTTTTTCAATCTAACTTTT
60 AATTTTTTAATCTC-A-C-TTTTACATTTATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTT
**
12204138 TAAATT
122 TACCTT
* * * * * * * *
12204144 TATAATTGAGGCTCCT-ATTTTTTCAATATCACTTTCTAGCTTTATAGTTGAAGCCCTTAATTTT
1 TATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTAAAGTCCTTAATTTT
* * * * *
12204208 TTAATCACATTTTTTTTTCATTTATAACT-AAGACTCCTAATTTTTTTCAATATCA--TTTTACC
66 TTAATCTCA---CTTTTACATTTATAATTGAAG-CTCCTAA-TTTTTTCAATCTCACTTTTTACC
12204270 TT
126 TT
* * *
12204272 CATAATTGAAGCCCCTAATTTTTTCAGTCTCACTTTTTTACCTTTATAATTAAAGTCCATAATTT
1 TATAATTGAAGCCCCTAATTTTTTCAATCTCAC-TTTTTACCTTTATAATTAAAGTCCTTAATTT
* * *
12204337 TTTAATCTCACTTTTACCTTTATAATTGATGCTCCTAATTTTTTCAATATCACTTTTTACCTT
65 TTTAATCTCACTTTTACATTTATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTTACCTT
* * * * * * *
12204400 TATAGTTGAAGCACATAATTTTTT-AATCTAATTTTTTACCTTTATAATTTAGGT-CTCTAATTT
1 TATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTAAAGTCCT-TAA-TT
** * * * *
12204463 TTTTCAATCTCACTTCCCACCTTTTATAATTGAAG-TGCTAATTTTTT-AATCTCGCTTTTTACT
64 TTTT-AATCTCACTT-TTA-CATTTATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTTACC
12204526 TT
126 TT
* * * *
12204528 TATAATTG-AGACCCCTAATTTTTCCAATGTAACTTTTTTACTTTTATAATT
1 TATAATTGAAG-CCCCTAATTTTTTCAATCTCAC-TTTTTACCTTTATAATT
12204579 TAGGACGCTA
Statistics
Matches: 449, Mismatches: 85, Indels: 65
0.75 0.14 0.11
Matches are distributed among these distances:
125 1 0.00
126 37 0.08
127 35 0.08
128 135 0.30
129 69 0.15
130 76 0.17
131 9 0.02
132 82 0.18
133 4 0.01
134 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (127 bp):
TATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTAAAGTCCTTAATTTT
TTAATCTCACTTTTACATTTATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTTACCTT
Found at i:12206727 original size:22 final size:22
Alignment explanation
Indices: 12206699--12206762 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 22
12206689 GACTTATTAT
12206699 TTTCGGTGGATTTAATTCCACC
1 TTTCGGTGGATTTAATTCCACC
* *
12206721 TTTCGGTGAAAATTTAATGCCACC
1 TTTCGGTG--GATTTAATTCCACC
12206745 TTTCGGTGGATTTTAATT
1 TTTCGGTGGA-TTTAATT
12206763 TTCAACAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.26
23 6 0.17
24 20 0.57
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (22 bp):
TTTCGGTGGATTTAATTCCACC
Found at i:12212325 original size:31 final size:31
Alignment explanation
Indices: 12212262--12212353 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 31
12212252 CTGATTCATA
* * *
12212262 GGTTAGTTTGATGTTTTATTTAAAATTCAAG
1 GGTTAATTTGATATTTTATGTAAAATTCAAG
* * *
12212293 GGTTAATTTGATATTTTGTGTAAAGTTTAAG
1 GGTTAATTTGATATTTTATGTAAAATTCAAG
* * * * *
12212324 GGTCAAATTGGTATTTTATCTAAACTTCAA
1 GGTTAATTTGATATTTTATGTAAAATTCAA
12212354 TGACCAAATT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.46
Consensus pattern (31 bp):
GGTTAATTTGATATTTTATGTAAAATTCAAG
Found at i:12212510 original size:22 final size:22
Alignment explanation
Indices: 12212485--12212535 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
12212475 TAAATTCAAT
12212485 GACCAAAAGTGCACACTTATGA
1 GACCAAAAGTGCACACTTATGA
12212507 GACCAAAAGTGCACACTTATGA
1 GACCAAAAGTGCACACTTATGA
12212529 GACCAAA
1 GACCAAA
12212536 GTGGCCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (22 bp):
GACCAAAAGTGCACACTTATGA
Found at i:12214657 original size:17 final size:18
Alignment explanation
Indices: 12214635--12214675 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
12214625 TTCAACAATA
12214635 AAAAAAGCCAA-AAAATC
1 AAAAAAGCCAAGAAAATC
12214652 AAAAAAGCCAAGAAAATC
1 AAAAAAGCCAAGAAAATC
12214670 AGAAAA
1 A-AAAA
12214676 CTTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 11 0.50
18 7 0.32
19 4 0.18
ACGTcount: A:0.71, C:0.15, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAAGCCAAGAAAATC
Found at i:12216270 original size:14 final size:13
Alignment explanation
Indices: 12216232--12216268 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
12216222 ATATATTAAT
* *
12216232 ATTTTCAAAAATC
1 ATTTTTAAAAACC
12216245 ATTTTTAAAAACC
1 ATTTTTAAAAACC
12216258 ATTTTTAAAAA
1 ATTTTTAAAAA
12216269 ACTGATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTTTTAAAAACC
Found at i:12216366 original size:70 final size:71
Alignment explanation
Indices: 12216287--12216448 Score: 236
Period size: 72 Copynumber: 2.3 Consensus size: 71
12216277 CAAAAATCGG
12216287 TTTAAAAACTATATAATATACGTTTTCAAAACTA-TTTTGAAAACTATATACTATATGTTTTCAA
1 TTTAAAAACTATATAATATACGTTTTCAAAACTATTTTTGAAAACTATATACTATATGTTTTCAA
*
12216351 AACTGT
66 AACTAT
* * * *
12216357 TTTAAAAACTATATATTTTACGTTTTCAAAACTATTTTTTTAAAACTATATATTATATGTTTTCA
1 TTTAAAAACTATATAATATACGTTTTCAAAACTA-TTTTTGAAAACTATATACTATATGTTTTCA
*
12216422 AAATTAT
65 AAACTAT
* *
12216429 CTTAAAAACTATATACTATA
1 TTTAAAAACTATATAATATA
12216449 TGATCGCTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 32 0.40
72 49 0.60
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44
Consensus pattern (71 bp):
TTTAAAAACTATATAATATACGTTTTCAAAACTATTTTTGAAAACTATATACTATATGTTTTCAA
AACTAT
Found at i:12216449 original size:35 final size:35
Alignment explanation
Indices: 12216287--12216450 Score: 211
Period size: 35 Copynumber: 4.6 Consensus size: 35
12216277 CAAAAATCGG
* *
12216287 TTTAAAAACTATATAATATACGTTTTCAAAACTAT
1 TTTAAAAACTATATACTATATGTTTTCAAAACTAT
* *
12216322 TTTGAAAACTATATACTATATGTTTTCAAAACTGT
1 TTTAAAAACTATATACTATATGTTTTCAAAACTAT
* * *
12216357 TTTAAAAACTATATATTTTACGTTTTCAAAACTATTT
1 TTTAAAAACTATATACTATATGTTTTCAAAACTA--T
* * *
12216394 TTTTAAAACTATATATTATATGTTTTCAAAATTAT
1 TTTAAAAACTATATACTATATGTTTTCAAAACTAT
*
12216429 CTTAAAAACTATATACTATATG
1 TTTAAAAACTATATACTATATG
12216451 ATCGCTTGTA
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
35 80 0.72
37 31 0.28
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTAAAAACTATATACTATATGTTTTCAAAACTAT
Found at i:12228467 original size:20 final size:22
Alignment explanation
Indices: 12228428--12228467 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12228418 TAAGTTTCCA
12228428 AAAACTATATATTATATATTTT
1 AAAACTATATATTATATATTTT
12228450 AAAACTATAT-TTAT-TATT
1 AAAACTATATATTATATATT
12228468 CTATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAACTATATATTATATATTTT
Found at i:12229248 original size:200 final size:201
Alignment explanation
Indices: 12228901--12229409 Score: 531
Period size: 200 Copynumber: 2.5 Consensus size: 201
12228891 TGAAAATTTC
** * * * * * * *
12228901 ACCAGAAAGTAGTTTATCACTGTTACCATGCGATTGATACGCCCTCAA-ACTAAATGGAATCGAA
1 ACCAGAAAGTAGTTCCTTACTGCTACCATACGATTGATATGTCTTCAAGA-TGAATGGAATCGAA
* * * * * **
12228965 CTCAAAAATTTTCGTTGACATATATCTCTTCTCGCCTTGAGCTATGCTATAAATTCGACTGGGAG
65 CTCAAAAATATTCATTAACAGATAACTCTTCTCGCCTTGAGCTATAATATAAATTCGACTGGGAG
* * * * * * *
12229030 ATAGTTCCTTGTTGCTAAATTGCAGCCAACTCAGAT-TTTTTCCTAACTTACACACCTTAGTTTA
130 ATAGTTCCTTGCTGCTAAATCGCAGCCAACCCAGATATTTTTCCTAACTTAAACACATCAATTTA
12229094 AACTTCA
195 AACTTCA
* *
12229101 ACCGGAAAGTAGTTCCTTACTGCTACCATACGATTGATATGTCTTCAAGATGAATGGAATTGAAC
1 ACCAGAAAGTAGTTCCTTACTGCTACCATACGATTGATATGTCTTCAAGATGAATGGAATCGAAC
* * * *
12229166 TCAAAAATATTCATTAACAGATAACTCTTTTCGCTTTGAGCTATAATGTAAATTCGATTGGGAGA
66 TCAAAAATATTCATTAACAGATAACTCTTCTCGCCTTGAGCTATAATATAAATTCGACTGGGAGA
* * *
12229231 TAGTTCCTTGCTGCTAAATCGCAGCTAACCCAGGTATTTTTCCTAACTTAAAGACATCAATTTAA
131 TAGTTCCTTGCTGCTAAATCGCAGCCAACCCAGATATTTTTCCTAACTTAAACACATCAATTTAA
12229296 ACTTCA
196 ACTTCA
* *** * * * * **
12229302 ACCAGAAAGTAGTTCATCGTTGCTACCATGC-ATTTGATACGCCTTCGAG-TGAATATAATCGAA
1 ACCAGAAAGTAGTTCCTTACTGCTACCATACGA-TTGATATGTCTTCAAGATGAATGGAATCGAA
* * * ** * *
12229365 CTCGAAAGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
65 CTCAAAAATATTCATTAACAGATAACTCTTCTCGCCTTGAGCTAT
12229410 GCTGTGAACA
Statistics
Matches: 253, Mismatches: 53, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
200 184 0.73
201 69 0.27
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (201 bp):
ACCAGAAAGTAGTTCCTTACTGCTACCATACGATTGATATGTCTTCAAGATGAATGGAATCGAAC
TCAAAAATATTCATTAACAGATAACTCTTCTCGCCTTGAGCTATAATATAAATTCGACTGGGAGA
TAGTTCCTTGCTGCTAAATCGCAGCCAACCCAGATATTTTTCCTAACTTAAACACATCAATTTAA
ACTTCA
Found at i:12237919 original size:6 final size:7
Alignment explanation
Indices: 12237868--12237922 Score: 51
Period size: 8 Copynumber: 7.4 Consensus size: 7
12237858 TGTTAAAATT
12237868 TAATAAA
1 TAATAAA
12237875 TAAATAAA
1 T-AATAAA
12237883 TAATAATA
1 TAATAA-A
12237891 TAACCT-AA
1 TAA--TAAA
12237899 TATATAAA
1 TA-ATAAA
12237907 TAATAAA
1 TAATAAA
12237914 -AATAAA
1 TAATAAA
12237920 TAA
1 TAA
12237923 AAAAAGTAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
6 6 0.15
7 14 0.34
8 18 0.44
9 2 0.05
10 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (7 bp):
TAATAAA
Found at i:12238089 original size:70 final size:71
Alignment explanation
Indices: 12238002--12238175 Score: 224
Period size: 72 Copynumber: 2.5 Consensus size: 71
12237992 AAAAAACTGA
* * * * * *
12238002 TTTCAAAACCGATTTAAAAACTATATACTATACGCTTTCAAAACTA-TTTTGAAAACTATATATT
1 TTTCAAAATCGTTTTAAAAACTATATAATATAAGCTTTCAAAAATATTTTTAAAAACTATATATT
12238066 ATATGT
66 ATATGT
* *
12238072 TTTCAAAATCGTTTTAAAAACTATATATTATAAGTTTTCAAAAATATTTTTTAAAAACTATATAT
1 TTTCAAAATCGTTTTAAAAACTATATAATATAAGCTTTCAAAAATA-TTTTTAAAAACTATATAT
12238137 TATATGT
65 TATATGT
** * *
12238144 TTTCAAAATTATCTGAAAAACTATATAATATA
1 TTTCAAAATCGTTTTAAAAACTATATAATATA
12238176 TTTTTTCAGA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
70 40 0.44
72 50 0.56
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (71 bp):
TTTCAAAATCGTTTTAAAAACTATATAATATAAGCTTTCAAAAATATTTTTAAAAACTATATATT
ATATGT
Found at i:12238148 original size:107 final size:105
Alignment explanation
Indices: 12238014--12238259 Score: 277
Period size: 107 Copynumber: 2.3 Consensus size: 105
12238004 TCAAAACCGA
* * * * *
12238014 TTTAAAAACTATATACTATACGCTTTCAAAACTATTTTG-AAAACTATATATTATATGTTTTCAA
1 TTTAAAAACTATATATTATATGATTTCAAAACTATTCTGAAAAACTATATAATATATGTTTTCAA
*
12238078 AATCGTTTTAAAAACTATATAT-TATAAGTTTTCAAAAAT-ATTT
66 AATCGTTTTAAAAA-TATATATGT-T--GTTTT-AAAAATAAGTT
* * * *
12238121 TTTAAAAACTATATATTATATGTTTTCAAAATTA-TCTGAAAAACTATATAATATATTTTTTCAG
1 TTTAAAAACTATATATTATATGATTTCAAAACTATTCTGAAAAACTATATAATATATGTTTTCAA
* *
12238185 AATGGTTTTAAAAATATATATGTTGTTTTAAAAGTAAGTT
66 AATCGTTTTAAAAATATATATGTTGTTTTAAAAATAAGTT
**
12238225 TCCAAAAACTATATATTATAT-ATTTCAAGAACTAT
1 TTTAAAAACTATATATTATATGATTTCAA-AACTAT
12238260 ATTTATTATG
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
103 11 0.09
104 31 0.26
106 11 0.09
107 66 0.55
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (105 bp):
TTTAAAAACTATATATTATATGATTTCAAAACTATTCTGAAAAACTATATAATATATGTTTTCAA
AATCGTTTTAAAAATATATATGTTGTTTTAAAAATAAGTT
Found at i:12238176 original size:35 final size:35
Alignment explanation
Indices: 12238013--12238245 Score: 190
Period size: 35 Copynumber: 6.7 Consensus size: 35
12238003 TTCAAAACCG
* * * *
12238013 ATTT-AAAAACTATATACTATACGCTTTCAAAACT
1 ATTTGAAAAACTATATATTATATGTTTTCAAAATT
*
12238047 ATTTTG-AAAACTATATATTATATGTTTTCAAAATC
1 A-TTTGAAAAACTATATATTATATGTTTTCAAAATT
* * *
12238082 GTTTTAAAAACTATATATTATAAGTTTTCAAAAATAT
1 ATTTGAAAAACTATATATTATATGTTTTC-AAAAT-T
* *
12238119 TTTTTAAAAACTATATATTATATGTTTTCAAAATT
1 ATTTGAAAAACTATATATTATATGTTTTCAAAATT
* * * * *
12238154 ATCTGAAAAACTATATAATATATTTTTTCAGAATG
1 ATTTGAAAAACTATATATTATATGTTTTCAAAATT
* * * *
12238189 GTTTTAAAAA-TATATA-TGT-TGTTTT-AAAAGTA
1 ATTTGAAAAACTATATATTATATGTTTTCAAAA-TT
*
12238221 AGTTTCCAAAAACTATATATTATAT
1 A-TTT-GAAAAACTATATATTATAT
12238246 ATTTCAAGAA
Statistics
Matches: 160, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
31 3 0.02
32 6 0.04
33 5 0.03
34 15 0.09
35 91 0.57
36 12 0.08
37 28 0.17
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.43
Consensus pattern (35 bp):
ATTTGAAAAACTATATATTATATGTTTTCAAAATT
Found at i:12238182 original size:72 final size:70
Alignment explanation
Indices: 12238017--12238205 Score: 211
Period size: 72 Copynumber: 2.7 Consensus size: 70
12238007 AAACCGATTT
* * * * *
12238017 AAAAACTATATACTATACGCTTTCAAAACTATTTTGAAAACTATATATTATATGTTTTCAAAATC
1 AAAAACTATATAATATAAGTTTTCAAAAATATTTTAAAAACTATATATTATATGTTTTCAAAATC
* * *
12238082 GTTTT
66 ATCTG
*
12238087 AAAAACTATATATTATAAGTTTTCAAAAATATTTTTTAAAAACTATATATTATATGTTTTCAAAA
1 AAAAACTATATAATATAAGTTTTCAAAAATA--TTTTAAAAACTATATATTATATGTTTTCAAAA
*
12238152 TTATCTG
64 TCATCTG
** * *
12238159 AAAAACTATATAATATATTTTTTC-AGAATGGTTTTAAAAA-TATATAT
1 AAAAACTATATAATATAAGTTTTCAAAAAT-ATTTTAAAAACTATATAT
12238206 GTTGTTTTAA
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
69 7 0.07
70 36 0.35
71 4 0.04
72 55 0.54
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (70 bp):
AAAAACTATATAATATAAGTTTTCAAAAATATTTTAAAAACTATATATTATATGTTTTCAAAATC
ATCTG
Found at i:12240899 original size:18 final size:18
Alignment explanation
Indices: 12240876--12240910 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12240866 ATGTTTTTCT
12240876 TATTATTTTTAATTTATC
1 TATTATTTTTAATTTATC
*
12240894 TATTATTTTTTATTTAT
1 TATTATTTTTAATTTAT
12240911 TGCATTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTATTTTTAATTTATC
Found at i:12258106 original size:36 final size:36
Alignment explanation
Indices: 12258059--12258161 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
12258049 ACATATTGTC
* *
12258059 TGTCTCCCTTGAGACAATTTCTCTTGAAACAAATTT
1 TGTCTCGCTTGAGACAGTTTCTCTTGAAACAAATTT
* *
12258095 TGTCTCGCTTGAGACCGTTTCTCTTAAAACAAATTT
1 TGTCTCGCTTGAGACAGTTTCTCTTGAAACAAATTT
**
12258131 TGTCTCGCTTGAGACAGTTTCTAATGAAACA
1 TGTCTCGCTTGAGACAGTTTCTCTTGAAACA
12258162 TAAAAATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (36 bp):
TGTCTCGCTTGAGACAGTTTCTCTTGAAACAAATTT
Found at i:12258218 original size:67 final size:67
Alignment explanation
Indices: 12258112--12258285 Score: 208
Period size: 67 Copynumber: 2.6 Consensus size: 67
12258102 CTTGAGACCG
** * *
12258112 TTTCTCTTAAAACAAA-TTTTGTCTCGCTTGAGACAGTTTCTAATGAAACATAAAAATTTTAGAT
1 TTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCTAATGAAACATAAAAATTTGAGAT
*
12258176 TG
66 TA
* ** **
12258178 TTTCTCTCGGAAA-AAAGTTTCGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
1 TTTCTCTC-GAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCTAATGAAACATAAAAATTTGAGA
12258242 TTA
65 TTA
* * *
12258245 TTTCTCTCGAAACAAAGTTTCGTCCCACTTGAGACAATTTC
1 TTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACAGTTTC
12258286 CCTTGATGCC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
66 14 0.15
67 77 0.85
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (67 bp):
TTTCTCTCGAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCTAATGAAACATAAAAATTTGAGAT
TA
Found at i:12258388 original size:102 final size:101
Alignment explanation
Indices: 12258236--12258548 Score: 367
Period size: 102 Copynumber: 3.1 Consensus size: 101
12258226 ACATAAACCT
** * * ** **
12258236 TTGAGATTATTTCTCTCGAAACAAAGTTTCGTCCCACTTGAGACAA-TTTCCCTTGATGCCCAAA
1 TTGAGATTATTT-TCTAAAAACAAA-TTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACAAAAA
* *
12258300 TTTCGAAGTTGTTTCACTTGAAACAAATTTGATCTCAC
64 TTTTGAAATTGTTTCACTTGAAACAAATTTGATCTCAC
* *
12258338 TTGAGATTATTTTCATAAAAACAAATTTCGTCTTGCTTGAGACAATTTTCCCTCGAAACAAAAAT
1 TTGAGATTATTTTC-TAAAAACAAATTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACAAAAAT
*
12258403 TTTGAAATTGTTTCACTTGAAACAAAATTGATCTCAC
65 TTTGAAATTGTTTCACTTGAAACAAATTTGATCTCAC
* * ** * * *
12258440 TTGAGATTGTTTTCCTGAAAACAAATTTTATCTCGCTTGAGATAGTTTTCTCTTGAAACAAAAAT
1 TTGAGATTATTTT-CTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACAAAAAT
* * *
12258505 TTTGAAATTGTTTCACTCGAAACAAATTTTATCTAAC
65 TTTGAAATTGTTTCACTTGAAACAAATTTGATCTCAC
*
12258542 CTGAGAT
1 TTGAGAT
12258549 AGCTTTCGCT
Statistics
Matches: 181, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
101 19 0.10
102 161 0.89
103 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (101 bp):
TTGAGATTATTTTCTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACAAAAATT
TTGAAATTGTTTCACTTGAAACAAATTTGATCTCAC
Found at i:12258462 original size:36 final size:37
Alignment explanation
Indices: 12258413--12258502 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 37
12258403 TTTGAAATTG
* *
12258413 TTTCACTTGAAACAAAATTGATCTCACTTGAGATTGT
1 TTTCTCTTGAAACAAAATTGATCTCACTTGAGATAGT
* * *
12258450 TTTC-C-TGAAAACAAATTTTATCTCGCTTGAGATAGT
1 TTTCTCTTG-AAACAAAATTGATCTCACTTGAGATAGT
12258486 TTTCTCTTGAAACAAAA
1 TTTCTCTTGAAACAAAA
12258503 ATTTTGAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
35 2 0.04
36 29 0.64
37 12 0.27
38 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAATTGATCTCACTTGAGATAGT
Found at i:12263616 original size:26 final size:24
Alignment explanation
Indices: 12263570--12263620 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 24
12263560 TTTATATCTT
12263570 TTAAAAATTATTTTTTATAAAAAA
1 TTAAAAATTATTTTTTATAAAAAA
12263594 TTAAAAATAGTATTTTATT-TAAAAAA
1 TTAAAAAT--TATTTT-TTATAAAAAA
12263620 T
1 T
12263621 CCAACTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 8 0.33
26 14 0.58
27 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAAAAATTATTTTTTATAAAAAA
Found at i:12263753 original size:167 final size:165
Alignment explanation
Indices: 12263459--12263784 Score: 476
Period size: 167 Copynumber: 2.0 Consensus size: 165
12263449 TAGGTATCTA
* ** *
12263459 TTTTATTGATTAATGTAGGTATCTAACATTTTCGACGTTATTATTTTAAGTTTATATGTCATAAA
1 TTTTATTGATTAATGTAGGTATCTAACATTTTCGACGTTACTATTTTAAGTGCATATATCATAAA
* **
12263524 CGCCTTTAAAAAATCTATTATCTAATATGTTTCATGTTTATATCTTTTAAAAATTATTTTTTATA
66 CGCCTTTAAAAAATCTATTATCTAATATGTGTCACATTTATATCTTTTAAAAATTATTTTTTAT-
*
12263589 AAAAATTAAAAATAGTATT-TTATTTAAAAAATCCAAC
130 AAAAA-TAAAAA-AATATTATTATTTAAAAAATCCAAC
* *
12263626 TTTTATTGATTAATGTAGGTATCTAATATTTTCGACGTTACTATTTTAAGTGCATATATCGTAAA
1 TTTTATTGATTAATGTAGGTATCTAACATTTTCGACGTTACTATTTTAAGTGCATATATCATAAA
* * * *
12263691 GGCCTTT-AAAATTTTATTATCTAATATGTGTCACATTTATATCTTTTAGAAATTATTTTTTTAT
66 CGCCTTTAAAAAATCTATTATCTAATATGTGTCACATTTATATCTTTTAAAAATTA-TTTTTTAT
12263755 AAAAATAAAAAAATATTATTATTTAAAAAA
130 AAAAATAAAAAAATATTATTATTTAAAAAA
12263785 GCCCAATTTT
Statistics
Matches: 143, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
164 5 0.03
165 18 0.13
166 47 0.33
167 73 0.51
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (165 bp):
TTTTATTGATTAATGTAGGTATCTAACATTTTCGACGTTACTATTTTAAGTGCATATATCATAAA
CGCCTTTAAAAAATCTATTATCTAATATGTGTCACATTTATATCTTTTAAAAATTATTTTTTATA
AAAATAAAAAAATATTATTATTTAAAAAATCCAAC
Found at i:12268318 original size:77 final size:77
Alignment explanation
Indices: 12268237--12268497 Score: 238
Period size: 77 Copynumber: 3.4 Consensus size: 77
12268227 CCATTTTTAT
* ** *
12268237 TGAAAGAGTTCATAGTGAGAAGAATTTGTTCGATTGTAGGTCATCCATTACAAAAGAAGGTGGAT
1 TGAAAGAGTTCATAATGAGAAGAATTTGTTCGACCGTAGGTCATCCATCACAAAAGAAGGTGGA-
12268302 TC-GTATTTCCAG
65 TCAGTATTTCCAG
* * * * * * * * * * * *
12268314 TGAAAAAGATCGTAATGAGAAAAACTTGTTCAACCCTAGCTCATTCATCACAAAAAACAGATAGA
1 TGAAAGAGTTCATAATGAGAAGAATTTGTTCGACCGTAGGTCATCCATCACAAAAGA-AGGTGGA
** *
12268379 TCACCATTTTCAG
65 TCAGTATTTCCAG
* * ** * * *
12268392 CGAAAGAATTCATAATGAGAAGAATTCATTCGACCG-AGGCTCATCCATCGCAGAAGGAGGTGGA
1 TGAAAGAGTTCATAATGAGAAGAATTTGTTCGACCGTAGG-TCATCCATCACAAAAGAAGGTGGA
12268456 TCAGTATTTCCAG
65 TCAGTATTTCCAG
*
12268469 TGAAGGAGTTCATAATGAGAAGAATTTGT
1 TGAAAGAGTTCATAATGAGAAGAATTTGT
12268498 GACTCAAAAG
Statistics
Matches: 135, Mismatches: 46, Indels: 6
0.72 0.25 0.03
Matches are distributed among these distances:
77 86 0.64
78 49 0.36
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (77 bp):
TGAAAGAGTTCATAATGAGAAGAATTTGTTCGACCGTAGGTCATCCATCACAAAAGAAGGTGGAT
CAGTATTTCCAG
Found at i:12268453 original size:155 final size:154
Alignment explanation
Indices: 12268161--12268472 Score: 351
Period size: 155 Copynumber: 2.0 Consensus size: 154
12268151 CTCGTCCAAA
* * * ** * * * **
12268161 GAAAAAGTTCGTAATGAGAATAACTTGTTTAACTTTGGCTTATCCATCACAGAAGGAGATTAATC
1 GAAAAAGATCGTAATGAGAAAAACTTGTTCAACCCTAGCTCATCCATCACAAAAACAGATTAATC
* ** * * ** ** *
12268226 ACCATTTTTATTGAAAGAGTTCATAGTGAGAAGAATTTGTTCGATTGTAGGTCATCCATTACAAA
66 ACCATTTTCAGCGAAAGAATTCATAATGAGAAGAATTCATTCGACCGTAGGTCATCCATCACAAA
12268291 AGAAGGTGGATTC-GTATTTCCAGT
131 AGAAGGTGGA-TCAGTATTTCCAGT
*
12268315 GAAAAAGATCGTAATGAGAAAAACTTGTTCAACCCTAGCTCATTCATCACAAAAAACAGA-TAGA
1 GAAAAAGATCGTAATGAGAAAAACTTGTTCAACCCTAGCTCATCCATCAC-AAAAACAGATTA-A
*
12268379 TCACCATTTTCAGCGAAAGAATTCATAATGAGAAGAATTCATTCGACCG-AGGCTCATCCATCGC
64 TCACCATTTTCAGCGAAAGAATTCATAATGAGAAGAATTCATTCGACCGTAGG-TCATCCATCAC
* *
12268443 AGAAGGAGGTGGATCAGTATTTCCAGT
128 AAAAGAAGGTGGATCAGTATTTCCAGT
12268470 GAA
1 GAA
12268473 GGAGTTCATA
Statistics
Matches: 130, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
154 49 0.38
155 81 0.62
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (154 bp):
GAAAAAGATCGTAATGAGAAAAACTTGTTCAACCCTAGCTCATCCATCACAAAAACAGATTAATC
ACCATTTTCAGCGAAAGAATTCATAATGAGAAGAATTCATTCGACCGTAGGTCATCCATCACAAA
AGAAGGTGGATCAGTATTTCCAGT
Found at i:12274178 original size:43 final size:43
Alignment explanation
Indices: 12274090--12274214 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 43
12274080 AAACGAGCAC
* * * * * * *
12274090 AAGATTGATGCTGATTCAACTCTTTTTGCGAAGAACCAAGCGA
1 AAGATTGTTACTGATCCAACTCCTTCTGTGAAGAATCAAGCGA
* *
12274133 AAGATT-TTCACTGATCTAACTCCTTCTGT-ATAGAATCAAGTGA
1 AAGATTGTT-ACTGATCCAACTCCTTCTGTGA-AGAATCAAGCGA
* *
12274176 AAGATTGTTATTGATCCAACTTCTTCTGTGAAGAATCAA
1 AAGATTGTTACTGATCCAACTCCTTCTGTGAAGAATCAA
12274215 ACAAAATGTC
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
42 2 0.03
43 61 0.92
44 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (43 bp):
AAGATTGTTACTGATCCAACTCCTTCTGTGAAGAATCAAGCGA
Found at i:12275708 original size:7 final size:7
Alignment explanation
Indices: 12275698--12275731 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
12275688 TTCCTTTTTC
12275698 TTCTTCT
1 TTCTTCT
12275705 TTCTTCT
1 TTCTTCT
12275712 TTCTTCTT
1 TTCTTC-T
12275720 TTCTTCT
1 TTCTTCT
12275727 TTCTT
1 TTCTT
12275732 TAAAAGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCTTCT
Found at i:12285111 original size:27 final size:28
Alignment explanation
Indices: 12285066--12285118 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
12285056 AGGGATTTTG
12285066 GTTTCAAAGGAAACCGACTCAAAGATTT
1 GTTTCAAAGGAAACCGACTCAAAGATTT
* *
12285094 GTTTCAAGGGAAA-TGACTCAAAGAT
1 GTTTCAAAGGAAACCGACTCAAAGAT
12285119 GACTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (28 bp):
GTTTCAAAGGAAACCGACTCAAAGATTT
Found at i:12285280 original size:35 final size:35
Alignment explanation
Indices: 12285233--12285324 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 35
12285223 CATTTCAAGG
12285233 GAAAC-GATCTCAAAGATGTTTGTTTTGTTT-C-AA
1 GAAACAGA-CTCAAAGATGTTTGTTTTGTTTCCAAA
* **
12285266 GTTAAATAGACTCAAAGATGGTAAGTTTTGTTTCCAAA
1 G--AAACAGACTCAAAGAT-GTTTGTTTTGTTTCCAAA
*
12285304 GAAACAGACTAAAAGATGTTT
1 GAAACAGACTCAAAGATGTTT
12285325 CTCAAAAGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
33 1 0.02
35 14 0.30
36 27 0.59
37 1 0.02
38 3 0.07
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (35 bp):
GAAACAGACTCAAAGATGTTTGTTTTGTTTCCAAA
Found at i:12285334 original size:28 final size:28
Alignment explanation
Indices: 12285294--12285429 Score: 73
Period size: 28 Copynumber: 4.6 Consensus size: 28
12285284 TGGTAAGTTT
12285294 TGTTTC-C-AAAGAAACAGACTAAAAGA
1 TGTTTCTCAAAAGAAACAGACTAAAAGA
*
12285320 TGTTTCTCAAAAGAAACTA-TCTCAAGAGAGACAA
1 TGTTTCTCAAAAGAAAC-AGACT-AA-A-AG---A
* * *
12285354 TTTTTTTCTTCTAAAGAAACAGACTCAAAGA
1 --TGTTTC-TCAAAAGAAACAGACTAAAAGA
* * *
12285385 TGTTTCTCAAAAGGAACAGAATCAAAGA
1 TGTTTCTCAAAAGAAACAGACTAAAAGA
*
12285413 T-TTGTTTCAAAAGAAAC
1 TGTT-TCTCAAAAGAAAC
12285430 TGTCTCAAGA
Statistics
Matches: 85, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
26 6 0.07
27 3 0.04
28 41 0.48
29 8 0.09
30 1 0.01
31 3 0.04
34 3 0.04
35 1 0.01
36 7 0.08
37 12 0.14
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.26
Consensus pattern (28 bp):
TGTTTCTCAAAAGAAACAGACTAAAAGA
Found at i:12285437 original size:28 final size:28
Alignment explanation
Indices: 12285366--12285429 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
12285356 TTTTTCTTCT
12285366 AAAGAAACAGACTCAAAGATGTTTCTCA
1 AAAGAAACAGACTCAAAGATGTTTCTCA
* * *
12285394 AAAGGAACAGAATCAAAGAT-TTGTTTCA
1 AAAGAAACAGACTCAAAGATGTT-TCTCA
12285422 AAAGAAAC
1 AAAGAAAC
12285430 TGTCTCAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (28 bp):
AAAGAAACAGACTCAAAGATGTTTCTCA
Found at i:12286145 original size:15 final size:15
Alignment explanation
Indices: 12286125--12286157 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12286115 ATGTAAATTT
12286125 TATGTATCATGTATG
1 TATGTATCATGTATG
*
12286140 TATGTATGATGTATG
1 TATGTATCATGTATG
12286155 TAT
1 TAT
12286158 TGATGTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TATGTATCATGTATG
Found at i:12286151 original size:11 final size:12
Alignment explanation
Indices: 12286137--12286167 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
12286127 TGTATCATGT
12286137 ATGTATGTA-TG
1 ATGTATGTATTG
12286148 ATGTATGTATTG
1 ATGTATGTATTG
12286160 ATGTATGT
1 ATGTATGT
12286168 TTTTCTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (12 bp):
ATGTATGTATTG
Found at i:12287373 original size:21 final size:21
Alignment explanation
Indices: 12287348--12287387 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12287338 TTGTCTGTAA
*
12287348 TTCTTGTCTTTTTTCTTTGCT
1 TTCTTGTCCTTTTTCTTTGCT
*
12287369 TTCTTTTCCTTTTTCTTTG
1 TTCTTGTCCTTTTTCTTTG
12287388 TTTTTGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.72
Consensus pattern (21 bp):
TTCTTGTCCTTTTTCTTTGCT
Found at i:12287375 original size:16 final size:16
Alignment explanation
Indices: 12287354--12287413 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
12287344 GTAATTCTTG
12287354 TCTTTTTTCTTTGCTT
1 TCTTTTTTCTTTGCTT
12287370 TCTTTTCCTT-TTT-CTT
1 TCTTTT--TTCTTTGCTT
* *
12287386 TGTTTTTGCTTTGCTCT
1 TCTTTTTTCTTTGCT-T
12287403 TCTTATTTTCT
1 TCTT-TTTTCT
12287414 CTTTGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 16 0.47
17 7 0.21
18 7 0.21
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.72
Consensus pattern (16 bp):
TCTTTTTTCTTTGCTT
Found at i:12287392 original size:31 final size:30
Alignment explanation
Indices: 12287357--12287425 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
12287347 ATTCTTGTCT
* *
12287357 TTTTTCTTTGCT-TTCTTTTCCTTTTTCTTTG
1 TTTTTCTTTGCTCTTCTTAT--TTTCTCTTTG
12287388 TTTTTGCTTTGCTCTTCTTATTTTCTCTTTG
1 TTTTT-CTTTGCTCTTCTTATTTTCTCTTTG
12287419 TTTTTCT
1 TTTTTCT
12287426 CTTAATTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 19 0.56
32 7 0.21
33 6 0.18
ACGTcount: A:0.01, C:0.19, G:0.07, T:0.72
Consensus pattern (30 bp):
TTTTTCTTTGCTCTTCTTATTTTCTCTTTG
Found at i:12287392 original size:32 final size:31
Alignment explanation
Indices: 12287356--12287428 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
12287346 AATTCTTGTC
* *
12287356 TTTTTTCTTTGCT-TTCTTTTCCTTTTTCTTTG
1 TTTTTTCTTTGCTCTTCTTAT--TTTCTCTTTG
*
12287388 TTTTTGCTTTGCTCTTCTTATTTTCTCTTTG
1 TTTTTTCTTTGCTCTTCTTATTTTCTCTTTG
12287419 TTTTTCTCTT
1 TTTTT-TCTT
12287429 AATTGCTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
31 14 0.40
32 15 0.43
33 6 0.17
ACGTcount: A:0.01, C:0.19, G:0.07, T:0.73
Consensus pattern (31 bp):
TTTTTTCTTTGCTCTTCTTATTTTCTCTTTG
Found at i:12287397 original size:11 final size:10
Alignment explanation
Indices: 12287378--12287473 Score: 51
Period size: 10 Copynumber: 9.7 Consensus size: 10
12287368 TTTCTTTTCC
12287378 TTTTTCTTTG
1 TTTTTCTTTG
12287388 TTTTTGCTTTG
1 TTTTT-CTTTG
* *
12287399 CTCTTCTTAT-
1 TTTTTCTT-TG
*
12287409 TTTCTCTTTG
1 TTTTTCTTTG
*
12287419 TTTTTCTCTTAA
1 TTTTTCT-TT-G
**
12287431 TTGCTCTTTG
1 TTTTTCTTTG
12287441 ---TT-TTT-
1 TTTTTCTTTG
12287446 TTTTTCTTTG
1 TTTTTCTTTG
12287456 TTTTTCTTTG
1 TTTTTCTTTG
12287466 ATTTTTCT
1 -TTTTTCT
12287474 CTCTTTGTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
6 3 0.05
7 1 0.02
8 2 0.03
9 4 0.06
10 29 0.45
11 20 0.31
12 5 0.08
ACGTcount: A:0.04, C:0.15, G:0.08, T:0.73
Consensus pattern (10 bp):
TTTTTCTTTG
Found at i:12287427 original size:25 final size:25
Alignment explanation
Indices: 12287390--12287513 Score: 107
Period size: 25 Copynumber: 5.1 Consensus size: 25
12287380 TTTCTTTGTT
* *
12287390 TTTGCTTTGCTCTTCTTAT-TTTCTC
1 TTTGTTTTTCTCTTCTT-TGTTTCTC
**
12287415 TTTGTTTTTCTCTTAATTG---CTC
1 TTTGTTTTTCTCTTCTTTGTTTCTC
* * *
12287437 TTTGTTTTTTTTTTCTTTGTTTTTC
1 TTTGTTTTTCTCTTCTTTGTTTCTC
12287462 TTTGATTTTTCTC-TCTTTGTTTCTC
1 TTTG-TTTTTCTCTTCTTTGTTTCTC
*
12287487 TTTGATTTTTCTC-TCTTTGTTTTTC
1 TTTG-TTTTTCTCTTCTTTGTTTCTC
12287512 TT
1 TT
12287514 ATCTCTTCGC
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
22 18 0.22
24 1 0.01
25 56 0.69
26 6 0.07
ACGTcount: A:0.04, C:0.17, G:0.08, T:0.71
Consensus pattern (25 bp):
TTTGTTTTTCTCTTCTTTGTTTCTC
Found at i:12287437 original size:22 final size:22
Alignment explanation
Indices: 12287403--12287445 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12287393 GCTTTGCTCT
* *
12287403 TCTTATTTTCTCTTTGTTTTTC
1 TCTTAATTGCTCTTTGTTTTTC
12287425 TCTTAATTGCTCTTTGTTTTT
1 TCTTAATTGCTCTTTGTTTTT
12287446 TTTTTCTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.70
Consensus pattern (22 bp):
TCTTAATTGCTCTTTGTTTTTC
Found at i:12287511 original size:14 final size:15
Alignment explanation
Indices: 12287460--12287512 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
12287450 TCTTTGTTTT
12287460 TCTTTGATTTTTCTC
1 TCTTTGATTTTTCTC
12287475 TCTTTG----TT-TC
1 TCTTTGATTTTTCTC
12287485 TCTTTGATTTTTCTC
1 TCTTTGATTTTTCTC
12287500 TCTTTG-TTTTTCT
1 TCTTTGATTTTTCT
12287513 TATCTCTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
14 9 0.27
15 14 0.42
ACGTcount: A:0.04, C:0.19, G:0.08, T:0.70
Consensus pattern (15 bp):
TCTTTGATTTTTCTC
Found at i:12289570 original size:27 final size:26
Alignment explanation
Indices: 12289532--12289587 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
12289522 AAGGATAAAA
12289532 AGTGACACAAACAAAATAA-ATAAGTT
1 AGTGACACAAACAAAA-AAGATAAGTT
*
12289558 AGTGTACACAAACAAAAAAGATTAGTT
1 AGTG-ACACAAACAAAAAAGATAAGTT
12289585 AGT
1 AGT
12289588 ACAAGTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (26 bp):
AGTGACACAAACAAAAAAGATAAGTT
Found at i:12289696 original size:32 final size:32
Alignment explanation
Indices: 12289660--12289739 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
12289650 TCATGATATT
*
12289660 TACCCGAACATGCTTTTATTAAATAGTAATCC
1 TACCCAAACATGCTTTTATTAAATAGTAATCC
*
12289692 TACCCAAACATGTTTTTATTAAATAGTAATCC
1 TACCCAAACATGCTTTTATTAAATAGTAATCC
*
12289724 TACCCAGACATG-TTTT
1 TACCCAAACATGCTTTT
12289740 CTACCCAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (32 bp):
TACCCAAACATGCTTTTATTAAATAGTAATCC
Found at i:12293999 original size:20 final size:20
Alignment explanation
Indices: 12293941--12293999 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
12293931 TTATATATTT
*
12293941 ATAATTAAAATAAAGATAATA
1 ATAAATAAAATAAA-ATAATA
* * *
12293962 AT-AGTGAAATAACGATAATA
1 ATAAATAAAATAA-AATAATA
12293982 ATAAATAAAATAAAATAA
1 ATAAATAAAATAAAATAA
12294000 AAAAGACCCG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (20 bp):
ATAAATAAAATAAAATAATA
Found at i:12300031 original size:41 final size:41
Alignment explanation
Indices: 12299986--12300103 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 41
12299976 ATCCTGCCTG
* * * *
12299986 AAGTCTTATGGATGGCCCGAATGTCTT-ATCATCTTTCTCGA
1 AAGTCTTAT-GATGGCCCGAAGGACTTAATCATCATGCTCGA
* *
12300027 AAGTCTTATAAATGGCCTGAAGGACTTAATCATCATGCTCGA
1 AAGTCTTAT-GATGGCCCGAAGGACTTAATCATCATGCTCGA
* *
12300069 AAGACTTACTGATGGCCCGAAGGACTTACTCATCA
1 AAGTCTTA-TGATGGCCCGAAGGACTTAATCATCA
12300104 AGAAACCCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 22 0.34
42 41 0.64
43 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (41 bp):
AAGTCTTATGATGGCCCGAAGGACTTAATCATCATGCTCGA
Found at i:12300410 original size:251 final size:251
Alignment explanation
Indices: 12299903--12300692 Score: 1025
Period size: 251 Copynumber: 3.1 Consensus size: 251
12299893 TATTGGCGAT
* *
12299903 GTTGGTCCCTCGAGTGAGGTGTTACTGATTCAACTCCATAAGTGATGAATCGAGTA-CTGGAAAT
1 GTTGGTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGTATC-GGAAAT
* *
12299967 GTTGAAAACATCCTGCCTGAA-GTCTTATGGATGGCCCGAATG-TCTTATCATCTTTCTCGAAAG
65 GTTGAAAACATCCTG-CTGAAGGTCTTATGGATGGCCCGAA-GAACTTATCATCTTGCTCGAAAG
* * * * *
12300030 TCTTATAAATGGCCTGAAGGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
128 ACTTATAGATGACC-GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGA----CCGAAGGACT
*
12300095 TACTCATCAAGAAACCCTTGAAAATCAAGATTAGTTTCTTAGTTGTCATCAATGAACCCCTACAT
188 TACTCAT------ACCCTTGAAAATCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACAT
12300160 ATCAC
247 ATCAC
* * * *
12300165 GTTGGTGCCTCGAGTGAGGTGTTGCTAATTCAACTCCATATGTGATTAATCAAGTATCGGAAATG
1 GTTGGTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCGGAAATG
* *
12300230 TTGAAAACATCCTGTCTGAAGGTGTTATGGATGGCCCGAAGAACTTATCATCTTGCTTGAAAGAC
66 TTGAAAACATCCTG-CTGAAGGTCTTATGGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGAC
* * * *
12300295 TTATAGATGACTCGAAGGATTTAAGCATCATGCTCAAAAGAATTACTGA-CAAAGAACTTACTCA
130 TTATAGATGAC-CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGACCGAAGGACTTACTCA
12300359 T-CCCTTGAAAATCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATCAC
194 TACCCTTGAAAATCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATCAC
* * *
12300416 GTTGGCCCCTTGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCAGAAATG
1 GTTGGTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCGGAAATG
*
12300481 TTGAAAACATCCTGCTCGAAGGTCTTATGGATGGCCTGAA-AGACTTATCATCTTGCTCGAAAGA
66 TTGAAAACATCCTGCT-GAAGGTCTTATGGATGGCCCGAAGA-ACTTATCATCTTGCTCGAAAGA
*
12300545 CTTATAGACGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGTCCCGAAGGACTT
129 CTTATAGATGA-CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGA----CCGAAGGACTT
* *
12300610 ACTCATCAATAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGCCATCAAGGAACCCCTACATA
189 A--C-TC-AT--ACCCTTGAAAATCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATA
12300675 TCAC
248 TCAC
*
12300679 ATTGGTCCCTCGAG
1 GTTGGTCCCTCGAG
12300693 CTTAGTTTCT
Statistics
Matches: 468, Mismatches: 41, Indels: 37
0.86 0.08 0.07
Matches are distributed among these distances:
250 3 0.01
251 214 0.46
252 1 0.00
256 9 0.02
258 15 0.03
259 2 0.00
260 2 0.00
262 77 0.16
263 144 0.31
264 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (251 bp):
GTTGGTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGTATCGGAAATG
TTGAAAACATCCTGCTGAAGGTCTTATGGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACT
TATAGATGACCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGACCGAAGGACTTACTCATA
CCCTTGAAAATCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATATCAC
Found at i:12300617 original size:42 final size:41
Alignment explanation
Indices: 12300522--12300617 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
12300512 TGGCCTGAAA
*
12300522 GACTTATCATCTTGCTCGAAAGACTTATAGACGACCCGAAG
1 GACTTATCATCATGCTCGAAAGACTTATAGACGACCCGAAG
* * * *
12300563 GATTTAAGCATCATGCTCGAAAGACTTACT-GATGTCCCGAAG
1 GACTT-ATCATCATGCTCGAAAGACTTA-TAGACGACCCGAAG
12300605 GACTTACTCATCA
1 GACTTA-TCATCA
12300618 ATAAACCCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 5 0.11
42 39 0.87
43 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
GACTTATCATCATGCTCGAAAGACTTATAGACGACCCGAAG
Found at i:12300771 original size:71 final size:71
Alignment explanation
Indices: 12300655--12300812 Score: 289
Period size: 71 Copynumber: 2.2 Consensus size: 71
12300645 TCTTAGTTGC
12300655 CATCAAGGAACCCCTACATATCACATTGGTCCCTCGAGCTTAGTTTCTTATAAAAATTCATTGAA
1 CATCAAGGAACCCCTACATATCACATTGGTCCCTCGAGCTTAGTTTCTTATAAAAATTCATTGAA
12300720 AATCAT
66 AATCAT
*
12300726 CATCAAGGAACCCCTACATATCACGTTGGTCCCTCGAGCTTAGTTTCTTATAAAAATTCATTGAA
1 CATCAAGGAACCCCTACATATCACATTGGTCCCTCGAGCTTAGTTTCTTATAAAAATTCATTGAA
*
12300791 AATCGT
66 AATCAT
*
12300797 CATCAAGAAACCCCTA
1 CATCAAGGAACCCCTA
12300813 AAAATTAGGC
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 84 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (71 bp):
CATCAAGGAACCCCTACATATCACATTGGTCCCTCGAGCTTAGTTTCTTATAAAAATTCATTGAA
AATCAT
Found at i:12300867 original size:112 final size:113
Alignment explanation
Indices: 12300725--12300944 Score: 388
Period size: 112 Copynumber: 2.0 Consensus size: 113
12300715 TTGAAAATCA
* *
12300725 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCGAGCTTAGTTTCTTATAAAAATTCATTGA
1 TCATCAAAGAACCCCTACATATCACGTTGGTCCCTCGACCTTAGTTTCTTATAAAAATTCATTGA
*
12300790 AAATCGTCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAGTTG
66 AAATCGTCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTAGTTG
*
12300838 TCATCAAAGAA-CCCTACATATCACGTTGGTCCCTCGACCTTAGTTTCTTGTAAAAATTCATTGA
1 TCATCAAAGAACCCCTACATATCACGTTGGTCCCTCGACCTTAGTTTCTTATAAAAATTCATTGA
*
12300902 AAATCGTCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTT
66 AAATCGTCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTT
12300945 TAAAAAATCT
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
112 92 0.90
113 10 0.10
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (113 bp):
TCATCAAAGAACCCCTACATATCACGTTGGTCCCTCGACCTTAGTTTCTTATAAAAATTCATTGA
AAATCGTCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTAGTTG
Found at i:12302894 original size:9 final size:9
Alignment explanation
Indices: 12302882--12302994 Score: 77
Period size: 10 Copynumber: 11.7 Consensus size: 9
12302872 ATCGATTTTC
12302882 TTTTTTCTT
1 TTTTTTCTT
12302891 TTTTTT-TT
1 TTTTTTCTT
*
12302899 TTTTCTATTTT
1 TTTT-T-TCTT
12302910 TTTCCTTTCTT
1 TTT--TTTCTT
*
12302921 TTTTTCCTTT
1 TTTTTTC-TT
12302931 TTTTTTCCTT
1 TTTTTT-CTT
*
12302941 TTTTCTCTT
1 TTTTTTCTT
12302950 TTTCTCTT-TT
1 TTT-T-TTCTT
*
12302960 TTCTTTCTT
1 TTTTTTCTT
*
12302969 TTTTATCTTT
1 TTTTTTC-TT
12302979 TTTATTTCTT
1 TTT-TTTCTT
12302989 TTTTTT
1 TTTTTT
12302995 TCTATATGTT
Statistics
Matches: 83, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
8 8 0.10
9 27 0.33
10 30 0.36
11 16 0.19
12 1 0.01
13 1 0.01
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:12302895 original size:8 final size:8
Alignment explanation
Indices: 12302877--12302993 Score: 82
Period size: 8 Copynumber: 14.5 Consensus size: 8
12302867 ATTTGATCGA
12302877 TTTTC-TT
1 TTTTCTTT
12302884 TTTTCTTT
1 TTTTCTTT
12302892 TTTT-TTT
1 TTTTCTTT
*
12302899 TTTTCTAT
1 TTTTCTTT
*
12302907 TTTT-TTC
1 TTTTCTTT
*
12302914 CTTTCTTT
1 TTTTCTTT
12302922 TTTTCCTTTTT
1 TTTT-C--TTT
*
12302933 TTTTCCTT
1 TTTTCTTT
*
12302941 TTTTCTCT
1 TTTTCTTT
12302949 TTTTCTCTT
1 TTTTCT-TT
12302958 TTTTCTTT
1 TTTTCTTT
12302966 CTTTT-TTAT
1 -TTTTCTT-T
*
12302975 CTTT-TTT
1 TTTTCTTT
*
12302982 ATTTCTTT
1 TTTTCTTT
12302990 TTTT
1 TTTT
12302994 TTCTATATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
7 20 0.23
8 46 0.53
9 13 0.15
10 1 0.01
11 7 0.08
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:12302912 original size:20 final size:19
Alignment explanation
Indices: 12302884--12302995 Score: 89
Period size: 20 Copynumber: 5.5 Consensus size: 19
12302874 CGATTTTCTT
12302884 TTTTCTTTTTTTTTTTTTTC
1 TTTT-TTTTTTTTTTTTTTC
12302904 TATTTTTTTCCTTTCTTTTTTTCC
1 T-TTTTTTT--TTT-TTTTTTT-C
* *
12302928 TTTTTTTTTCCTTTTTTCTC
1 TTTTTTTTT-TTTTTTTTTC
* * *
12302948 TTTTTCTCTTTTTTCTTTC
1 TTTTTTTTTTTTTTTTTTC
* *
12302967 TTTTTTATCTTTTTTATTTC
1 TTTTTT-TTTTTTTTTTTTC
12302987 TTTTTTTTT
1 TTTTTTTTT
12302996 CTATATGTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
19 14 0.19
20 31 0.41
21 10 0.13
22 4 0.05
23 14 0.19
24 2 0.03
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTTTC
Found at i:12303008 original size:48 final size:45
Alignment explanation
Indices: 12302877--12303015 Score: 136
Period size: 48 Copynumber: 3.0 Consensus size: 45
12302867 ATTTGATCGA
* * *
12302877 TTTTCTTTTTTCTTT-TTTTTTTTTTTCTATTTTTTTCCTTTCTTT
1 TTTTCTTTTTT-TTTCTTTTTTTTTCTATATTTTTTTTCTTTCTTT
* * * *
12302922 TTTTCCTTTTTTTTTCCTTTTTTCTCTTTTTCTCTTTTTTCTTTCTTT
1 TTTT-CTTTTTTTTTCTTTTTTTTTCTATAT-T-TTTTTTCTTTCTTT
*
12302970 TTTATCTTTTTTATTTCTTTTTTTTTCTATATGTTTTTTTGTTTCT
1 TTT-TCTTTTTT-TTTCTTTTTTTTTCTATAT-TTTTTTTCTTTCT
12303016 ATCTGTGTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
45 7 0.09
46 17 0.22
47 1 0.01
48 34 0.45
49 17 0.22
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (45 bp):
TTTTCTTTTTTTTTCTTTTTTTTTCTATATTTTTTTTCTTTCTTT
Found at i:12304728 original size:141 final size:140
Alignment explanation
Indices: 12304452--12304732 Score: 406
Period size: 141 Copynumber: 2.0 Consensus size: 140
12304442 GTTCCTTAAA
12304452 CAATTCTTGAAAAACGAAAATGTCTCGATACACTAGGGAAGTGAAGATCTGGTCCATCTGTAAGT
1 CAATTCTTGAAAAACGAAAATGTCTCGATACACTAGGGAAGTGAAGATCTGGTCCATCTGTAAGT
* * * **
12304517 CGCCTAGCTCCTGCGAGTATCTGGGTACTGCGTCATCTTCAAAGCTTATACTTCATCTCCTACTT
66 CACCTAGCTCCTACGAGCATCTGGGTACTGCGTCATCTTCAAAGCTTATACTTCAGATCCTACTT
12304582 CCAGAAATCT
131 CCAGAAATCT
* * *
12304592 CAATTCTTGAAAAACTGACAATGTCTCTG-TACA-TGGGGGAAGTGAAGATCTGGTCCATTTGTA
1 CAATTCTTGAAAAAC-GAAAATGTCTC-GATACACT-AGGGAAGTGAAGATCTGGTCCATCTGTA
* *
12304655 AGTCACCTAGCTCAC-ACGAGCATCTGGGTACTGCGTCGTCTTCAAAGCTTATACTTCAGATCTT
63 AGTCACCTAGCTC-CTACGAGCATCTGGGTACTGCGTCATCTTCAAAGCTTATACTTCAGATCCT
*
12304719 ACTTTCAGAAATCT
127 ACTTCCAGAAATCT
12304733 TTCAAGCTGG
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
140 16 0.13
141 108 0.86
142 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (140 bp):
CAATTCTTGAAAAACGAAAATGTCTCGATACACTAGGGAAGTGAAGATCTGGTCCATCTGTAAGT
CACCTAGCTCCTACGAGCATCTGGGTACTGCGTCATCTTCAAAGCTTATACTTCAGATCCTACTT
CCAGAAATCT
Found at i:12305037 original size:31 final size:29
Alignment explanation
Indices: 12304997--12305054 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
12304987 AAATGTAACA
*
12304997 AGACCAGACAAAAAGAAATCAATGTTAGTAG
1 AGACAAGACAAAAAG-AATCAA-GTTAGTAG
12305028 AGACAAGACAAAAAGAATCAAGTTAGT
1 AGACAAGACAAAAAGAATCAAGTTAGT
12305055 TGAAATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.23
30 6 0.23
31 14 0.54
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (29 bp):
AGACAAGACAAAAAGAATCAAGTTAGTAG
Found at i:12308317 original size:26 final size:25
Alignment explanation
Indices: 12308288--12308358 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 25
12308278 GGTGCAGAGG
12308288 ATGGTGGTGTCTGATTGGGGCAGCAA
1 ATGGTGGTGT-TGATTGGGGCAGCAA
12308314 ATGGTGGTGTTTGATTGGGGCAGCAA
1 ATGGTGGTG-TTGATTGGGGCAGCAA
12308340 ATGGTGGATGTTGATTGGG
1 ATGGTGG-TGTTGATTGGG
12308359 CACTGGGTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 40 0.93
27 3 0.07
ACGTcount: A:0.18, C:0.07, G:0.44, T:0.31
Consensus pattern (25 bp):
ATGGTGGTGTTGATTGGGGCAGCAA
Found at i:12308454 original size:24 final size:24
Alignment explanation
Indices: 12308425--12308478 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
12308415 GGTCTTGGCT
12308425 TGGGTTTAGGGT-TTGGTTGTAAAA
1 TGGGTTTA-GGTATTGGTTGTAAAA
* *
12308449 TGGGTTTAGGTATTGGTTTTAAAT
1 TGGGTTTAGGTATTGGTTGTAAAA
12308473 TGGGTT
1 TGGGTT
12308479 ATATTTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (24 bp):
TGGGTTTAGGTATTGGTTGTAAAA
Found at i:12310787 original size:89 final size:90
Alignment explanation
Indices: 12310574--12310798 Score: 416
Period size: 90 Copynumber: 2.5 Consensus size: 90
12310564 ATAAATTAAC
*
12310574 AACCAATATTATTCTATTTTCTTCCCTTTTAACATTAGGCTTTTAGCAATTAAATATATTCATAA
1 AACCAATATTATTCTATTTTCTTCCCTTTTAACACTAGGCTTTTAGCAATTAAATATATTCATAA
*
12310639 ATATTTACCCCCGCATAATAATAAA
66 ATATTTAACCCCGCATAATAATAAA
*
12310664 AATCAATATTATTCTATTTTCTTCCCTTTTAACACTAGGCTTTTAGCAATTAAATATATTCATAA
1 AACCAATATTATTCTATTTTCTTCCCTTTTAACACTAGGCTTTTAGCAATTAAATATATTCATAA
12310729 ATA-TTAACCCCGCATAATAATAAA
66 ATATTTAACCCCGCATAATAATAAA
12310753 AACCAATATTATTCTATTTTCTTCCCTTTTAACACTAGGCTTTTAG
1 AACCAATATTATTCTATTTTCTTCCCTTTTAACACTAGGCTTTTAG
12310799 TAATAATAAT
Statistics
Matches: 131, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 65 0.50
90 66 0.50
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (90 bp):
AACCAATATTATTCTATTTTCTTCCCTTTTAACACTAGGCTTTTAGCAATTAAATATATTCATAA
ATATTTAACCCCGCATAATAATAAA
Found at i:12311783 original size:14 final size:14
Alignment explanation
Indices: 12311750--12311791 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
12311740 CGAAATACAA
12311750 AAATCAGATATCAGG
1 AAATCA-ATATCAGG
12311765 AAATCAATATTCAGG
1 AAATCAATA-TCAGG
12311780 -AATCAAGTATCA
1 AAATCAA-TATCA
12311792 TGTCATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (14 bp):
AAATCAATATCAGG
Found at i:12312683 original size:29 final size:29
Alignment explanation
Indices: 12312633--12312701 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
12312623 TATCATCACG
* *
12312633 AAAATAACACCATTTTCAAAATAATTACC
1 AAAATAGCACCATTTCCAAAATAATTACC
* *
12312662 AGAATAGCACCATTTCCCAAATAATTACC
1 AAAATAGCACCATTTCCAAAATAATTACC
12312691 AAAATAGCACC
1 AAAATAGCACC
12312702 CAGTCAACGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (29 bp):
AAAATAGCACCATTTCCAAAATAATTACC
Found at i:12312763 original size:9 final size:9
Alignment explanation
Indices: 12312745--12312791 Score: 67
Period size: 9 Copynumber: 5.0 Consensus size: 9
12312735 GTCGGGTTGC
12312745 AACCGGTCA
1 AACCGGTCA
*
12312754 AACGGGTCA
1 AACCGGTCA
12312763 AACCGGTTCAA
1 AACCGG-TC-A
12312774 AACCGGTCA
1 AACCGGTCA
12312783 AACCGGTCA
1 AACCGGTCA
12312792 TTTTTACCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 23 0.68
10 4 0.12
11 7 0.21
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.13
Consensus pattern (9 bp):
AACCGGTCA
Found at i:12312781 original size:20 final size:19
Alignment explanation
Indices: 12312745--12312789 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
12312735 GTCGGGTTGC
*
12312745 AACCGG-TCAAACGGGTCA
1 AACCGGTTCAAACCGGTCA
12312763 AACCGGTTCAAAACCGGTCA
1 AACCGGTTC-AAACCGGTCA
12312783 AACCGGT
1 AACCGGT
12312790 CATTTTTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 16 0.67
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.13
Consensus pattern (19 bp):
AACCGGTTCAAACCGGTCA
Found at i:12313854 original size:17 final size:17
Alignment explanation
Indices: 12313832--12313870 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
12313822 TGCTGGGGAG
12313832 GCAACTCAAGCTGATAA
1 GCAACTCAAGCTGATAA
12313849 GCAACTCAAGCTGATAA
1 GCAACTCAAGCTGATAA
12313866 GCAAC
1 GCAAC
12313871 AGGTCCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (17 bp):
GCAACTCAAGCTGATAA
Found at i:12317621 original size:35 final size:35
Alignment explanation
Indices: 12317582--12317656 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
12317572 AAATCTTGAT
12317582 TTTGAGCTCGATTCAAGCTCAAACTCGAA-CTCAAA
1 TTTGAGCTCGATTCAAGCTCAAACTC-AAGCTCAAA
* *
12317617 TTTGAGCTCGATTCAAGCTCGAACTCAAGCTCGAA
1 TTTGAGCTCGATTCAAGCTCAAACTCAAGCTCAAA
12317652 TTTGA
1 TTTGA
12317657 ACCTACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (35 bp):
TTTGAGCTCGATTCAAGCTCAAACTCAAGCTCAAA
Found at i:12320308 original size:7 final size:7
Alignment explanation
Indices: 12320296--12320400 Score: 52
Period size: 7 Copynumber: 14.9 Consensus size: 7
12320286 GTACATAACT
12320296 TAAACCC
1 TAAACCC
12320303 TAAACCC
1 TAAACCC
*
12320310 TAAATCC
1 TAAACCC
*
12320317 TAACCCC
1 TAAACCC
**
12320324 TAATA-TA
1 TAA-ACCC
*
12320331 TGAACCC
1 TAAACCC
*
12320338 TAAACAC
1 TAAACCC
12320345 TAAACCC
1 TAAACCC
* *
12320352 TAAATCA
1 TAAACCC
* *
12320359 T-ATCACA
1 TAAAC-CC
12320366 TAAAACCC
1 T-AAACCC
*
12320374 TAAATCC
1 TAAACCC
*
12320381 TAAACTC
1 TAAACCC
*
12320388 TAAACCT
1 TAAACCC
12320395 TAAACC
1 TAAACC
12320401 TTATTATATA
Statistics
Matches: 70, Mismatches: 23, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
6 2 0.03
7 64 0.91
8 2 0.03
9 2 0.03
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:12320325 original size:21 final size:21
Alignment explanation
Indices: 12320296--12320398 Score: 66
Period size: 21 Copynumber: 4.9 Consensus size: 21
12320286 GTACATAACT
12320296 TAAACCCTAAACCCTAAATCC
1 TAAACCCTAAACCCTAAATCC
* ** * *
12320317 TAACCCCTAATA-TATGAACCC
1 TAAACCCTAA-ACCCTAAATCC
* *
12320338 TAAACACTAAACCCTAAATCA
1 TAAACCCTAAACCCTAAATCC
* *
12320359 T-ATCACATAAAACCCTAAATCC
1 TAAAC-CCT-AAACCCTAAATCC
* *
12320381 TAAACTCTAAACCTTAAA
1 TAAACCCTAAACCCTAAA
12320399 CCTTATTATA
Statistics
Matches: 57, Mismatches: 20, Indels: 10
0.66 0.23 0.11
Matches are distributed among these distances:
20 3 0.05
21 37 0.65
22 15 0.26
23 2 0.04
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATCC
Found at i:12320385 original size:14 final size:14
Alignment explanation
Indices: 12320368--12320433 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
12320358 ATATCACATA
*
12320368 AAACCCTAAATCCT
1 AAACCCTAAATCAT
* * *
12320382 AAACTCTAAACCTT
1 AAACCCTAAATCAT
* *
12320396 AAACCTTATTAT-AT
1 AAACCCTA-AATCAT
*
12320410 AAACTCTAAATCAT
1 AAACCCTAAATCAT
12320424 AAACCCTAAA
1 AAACCCTAAA
12320434 CCTTATCACA
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
13 2 0.05
14 35 0.92
15 1 0.03
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:12320391 original size:22 final size:21
Alignment explanation
Indices: 12320336--12320391 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
12320326 ATATATGAAC
12320336 CCTAAACACT-AAACCCTAAAT
1 CCTAAAC-CTAAAACCCTAAAT
* * *
12320357 CATATCACATAAAACCCTAAAT
1 CCTA-AACCTAAAACCCTAAAT
12320379 CCTAAACTCTAAA
1 CCTAAAC-CTAAA
12320392 CCTTAAACCT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (21 bp):
CCTAAACCTAAAACCCTAAAT
Found at i:12321161 original size:14 final size:14
Alignment explanation
Indices: 12321144--12321184 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12321134 TTTATTCATC
12321144 AATAATGTATTTTT
1 AATAATGTATTTTT
12321158 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
12321169 AATAATGTAATTTT
1 AATAATGTATTTTT
12321183 AA
1 AA
12321185 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:12322394 original size:14 final size:14
Alignment explanation
Indices: 12322360--12322402 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
12322350 CCGAAATACA
12322360 GAAATCAGATATCAG
1 GAAATCA-ATATCAG
12322375 GAAATCAATATTCAG
1 GAAATCAATA-TCAG
12322390 G-AATCAAGTATCA
1 GAAATCAA-TATCA
12322403 TGTATCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (14 bp):
GAAATCAATATCAG
Found at i:12323178 original size:29 final size:29
Alignment explanation
Indices: 12323144--12323334 Score: 138
Period size: 29 Copynumber: 6.6 Consensus size: 29
12323134 CATTTTTTTA
* * *
12323144 AATTACGAAAATAACACCATTTTGAAATT
1 AATTACCAAAATAACACCATTTTCAAAAT
* *
12323173 AATTACCAAAATAGCATCATTTTCAAAAT
1 AATTACCAAAATAACACCATTTTCAAAAT
* * *
12323202 AATTACTAAAATATCACTC-TTTT-AAAAA
1 AATTACCAAAATAACAC-CATTTTCAAAAT
** * * *
12323230 AATTA-CAAAATTGTCA-CTTTTTTAAAAA
1 AATTACCAAAA-TAACACCATTTTCAAAAT
* * *
12323258 AATTTACAAAAATAGCACCCTTTTCAAAAT
1 AA-TTACCAAAATAACACCATTTTCAAAAT
* * * *
12323288 AATTACCAGAATAGCACCATTTCCTAAAT
1 AATTACCAAAATAACACCATTTTCAAAAT
*
12323317 AATTACCAAAATAGCACC
1 AATTACCAAAATAACACC
12323335 CGATCAACGT
Statistics
Matches: 132, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.01
27 8 0.06
28 20 0.15
29 87 0.66
30 16 0.12
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (29 bp):
AATTACCAAAATAACACCATTTTCAAAAT
Found at i:12323328 original size:58 final size:56
Alignment explanation
Indices: 12323144--12323335 Score: 172
Period size: 58 Copynumber: 3.3 Consensus size: 56
12323134 CATTTTTTTA
* * * * *
12323144 AATTACGAAAATAACACCATTTTGAAATTAATTACCAAAATAGCATCATTTTCAAAAT
1 AATTACAAAAATAGCACCCTTTT-AAAATAATTACCAAAATAGCA-CATTTTCTAAAT
* * * * * * *
12323202 AATTACTAAAATATCACTCTTTTAAAAAAATTA-CAAAATTGTCAC-TTTTTTAAAAA
1 AATTACAAAAATAGCACCCTTTTAAAATAATTACCAAAATAG-CACATTTTCT-AAAT
* *
12323258 AATTTACAAAAATAGCACCCTTTTCAAAATAATTACCAGAATAGCACCATTTCCTAAAT
1 AA-TTACAAAAATAGCACCCTTTT-AAAATAATTACCAAAATAGCA-CATTTTCTAAAT
*
12323317 AATTACCAAAATAGCACCC
1 AATTACAAAAATAGCACCC
12323336 GATCAACGTT
Statistics
Matches: 107, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
55 4 0.04
56 13 0.12
57 28 0.26
58 46 0.43
59 12 0.11
60 4 0.04
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (56 bp):
AATTACAAAAATAGCACCCTTTTAAAATAATTACCAAAATAGCACATTTTCTAAAT
Found at i:12323366 original size:5 final size:5
Alignment explanation
Indices: 12323356--12323416 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
12323346 CAAAAGTTAA
* *
12323356 CGGGT CGGGT CGGGT CGGGT CAACGGGT CGAGT CGGGT C--AT CGGGT
1 CGGGT CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT CGGGT CGGGT
12323402 CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT
12323417 TGCAACCGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
3 2 0.04
5 40 0.85
8 5 0.11
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:12323384 original size:18 final size:18
Alignment explanation
Indices: 12323361--12323412 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
12323351 GTTAACGGGT
12323361 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
* *
12323379 CGGGTCGAGTCGGGTCAT
1 CGGGTCGGGTCGGGTCAA
12323397 CGGGTCGGGTCGGGTC
1 CGGGTCGGGTCGGGTC
12323413 GGGTTGCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTCAA
Found at i:12327618 original size:22 final size:21
Alignment explanation
Indices: 12327578--12327618 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12327568 TTTTTAAATA
* *
12327578 ATTTTTATAAGTATCATATTT
1 ATTTTTATAAATATAATATTT
12327599 ATTTTTATAAAATATAATAT
1 ATTTTTAT-AAATATAATAT
12327619 AATATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTTTATAAATATAATATTT
Found at i:12330035 original size:92 final size:92
Alignment explanation
Indices: 12329878--12330063 Score: 372
Period size: 92 Copynumber: 2.0 Consensus size: 92
12329868 ACCAAACATC
12329878 ACATCCTGAAAATTAAGCAAAAAAGATTTATGTAAAACAATCTAGTATGTAATTACATGCATTTA
1 ACATCCTGAAAATTAAGCAAAAAAGATTTATGTAAAACAATCTAGTATGTAATTACATGCATTTA
12329943 TGCATTACGTGGAAAGGAAGTAATCGT
66 TGCATTACGTGGAAAGGAAGTAATCGT
12329970 ACATCCTGAAAATTAAGCAAAAAAGATTTATGTAAAACAATCTAGTATGTAATTACATGCATTTA
1 ACATCCTGAAAATTAAGCAAAAAAGATTTATGTAAAACAATCTAGTATGTAATTACATGCATTTA
12330035 TGCATTACGTGGAAAGGAAGTAATCGT
66 TGCATTACGTGGAAAGGAAGTAATCGT
12330062 AC
1 AC
12330064 CATGATAATG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.29
Consensus pattern (92 bp):
ACATCCTGAAAATTAAGCAAAAAAGATTTATGTAAAACAATCTAGTATGTAATTACATGCATTTA
TGCATTACGTGGAAAGGAAGTAATCGT
Found at i:12331445 original size:60 final size:60
Alignment explanation
Indices: 12331381--12331502 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
12331371 ACCATTTTAT
* * * * *
12331381 ATTAGTTCTTAAAG-TTTTAAATATACTAATTTCATCCTCAAATTATGAATTTCATTCTAA
1 ATTAGTCCTT-AAGCTTTTAAACATACCAATTTCATCCCCAAATTATGAATCTCATTCTAA
* *
12331441 ATTAGTCCTTAAGCTTTTGAACATTCCAATTTCATCCCCAAATTATGAATCTCATTCTAA
1 ATTAGTCCTTAAGCTTTTAAACATACCAATTTCATCCCCAAATTATGAATCTCATTCTAA
12331501 AT
1 AT
12331503 GGGTCACTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 3 0.06
60 51 0.94
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (60 bp):
ATTAGTCCTTAAGCTTTTAAACATACCAATTTCATCCCCAAATTATGAATCTCATTCTAA
Found at i:12333071 original size:21 final size:21
Alignment explanation
Indices: 12333045--12333117 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
12333035 TTCCAGATTT
*
12333045 GCAACGCGAACTTCGACTATC
1 GCAACGCGAACTTGGACTATC
12333066 GCAACGCGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
* *
12333087 GCAATGTGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
*
12333108 GCAATGCGAA
1 GCAACGCGAA
12333118 TATGTAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (21 bp):
GCAACGCGAACTTGGACTATC
Found at i:12333130 original size:42 final size:42
Alignment explanation
Indices: 12333045--12333177 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 42
12333035 TTCCAGATTT
* * * * **
12333045 GCAACGCGAACTTCGACTATCGCAACGCGAACT-TGGACTATC
1 GCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTAAAATC
*
12333087 GCAATGTGAACTTGGACTATCGCAATGCGAATATGTAAAATC
1 GCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAAATC
* *
12333129 GCAATGCGAA-TATGTA-AATCGCAATGCGAATATGT-AAATC
1 GCAATGCGAACT-TGGACTATCGCAATGCGAATATGTAAAATC
12333169 GCAATGCGA
1 GCAATGCGA
12333178 TAGTCGACTA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 14 0.18
41 20 0.25
42 45 0.57
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (42 bp):
GCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAAATC
Found at i:12333149 original size:20 final size:20
Alignment explanation
Indices: 12333105--12333177 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
12333095 AACTTGGACT
12333105 ATCGCAATGCGAATATGTAAA
1 ATCGCAATGCGAATATGT-AA
12333126 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
12333146 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
12333166 ATCGCAATGCGA
1 ATCGCAATGCGA
12333178 TAGTCGACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
20 34 0.65
21 18 0.35
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:12333234 original size:20 final size:20
Alignment explanation
Indices: 12333209--12333322 Score: 110
Period size: 20 Copynumber: 5.6 Consensus size: 20
12333199 ACTTGGACTA
12333209 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
12333229 TCGCATTGCGATAGT-CGACT-G
1 TCGCATTGCGAT-TTAC-A-TAT
12333250 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
12333270 TCGCATTGCGATAGT-CGACT-G
1 TCGCATTGCGAT-TTAC-A-TAT
12333291 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
12333311 TCGCATTGCGAT
1 TCGCATTGCGAT
12333323 AGTCGACTGT
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.03
20 42 0.55
21 30 0.39
22 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:12333255 original size:21 final size:21
Alignment explanation
Indices: 12333229--12333388 Score: 154
Period size: 21 Copynumber: 7.7 Consensus size: 21
12333219 ATTTACATAT
12333229 TCGCATTGCGATAGTCGACTG
1 TCGCATTGCGATAGTCGACTG
* *
12333250 TCGCATTGCGAT--T-TACATAT
1 TCGCATTGCGATAGTCGAC-T-G
12333270 TCGCATTGCGATAGTCGACTG
1 TCGCATTGCGATAGTCGACTG
* *
12333291 TCGCATTGCGAT--T-TACATAT
1 TCGCATTGCGATAGTCGAC-T-G
12333311 TCGCATTGCGATAGTCGACTG
1 TCGCATTGCGATAGTCGACTG
* *
12333332 TCGCATTGCGATAGTCCA-AG
1 TCGCATTGCGATAGTCGACTG
*
12333352 TTCGCATTGCGATAGTCGACTA
1 -TCGCATTGCGATAGTCGACTG
*
12333374 TCGCTTTGCGATAGT
1 TCGCATTGCGATAGT
12333389 TCAAAATCGC
Statistics
Matches: 113, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
18 4 0.04
19 4 0.04
20 25 0.22
21 72 0.64
22 4 0.04
23 4 0.04
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGACTG
Found at i:12333255 original size:41 final size:41
Alignment explanation
Indices: 12333204--12333385 Score: 294
Period size: 41 Copynumber: 4.4 Consensus size: 41
12333194 TTCGAACTTG
*
12333204 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTGTCGCATTGCGATTTACATATTCGCATTGCGATAGTC
12333245 GACTGTCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTGTCGCATTGCGATTTACATATTCGCATTGCGATAGTC
12333286 GACTGTCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTGTCGCATTGCGATTTACATATTCGCATTGCGATAGTC
* *
12333327 GACTGTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTC
1 GACTGTCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTC
* *
12333369 GACTATCGCTTTGCGAT
1 GACTGTCGCATTGCGAT
12333386 AGTTCAAAAT
Statistics
Matches: 134, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
41 99 0.74
42 35 0.26
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (41 bp):
GACTGTCGCATTGCGATTTACATATTCGCATTGCGATAGTC
Found at i:12333397 original size:21 final size:21
Alignment explanation
Indices: 12333332--12333399 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
12333322 TAGTCGACTG
* **
12333332 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTTCAAAA
**
12333353 TCGCATTGCGATAG-TCGACTA
1 TCGCATTGCGATAGTTC-AAAA
*
12333374 TCGCTTTGCGATAGTTCAAAA
1 TCGCATTGCGATAGTTCAAAA
12333395 TCGCA
1 TCGCA
12333400 ACGAATGGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 34 0.92
22 2 0.05
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTTCAAAA
Found at i:12333501 original size:6 final size:6
Alignment explanation
Indices: 12333490--12333549 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
12333480 TTACCATGAA
* *
12333490 CACGAC CACGAC CACAAC CACGAC CACGAC CACGAC CACGAC CACAAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
12333538 CACGAC C-CGAC C
1 CACGAC CACGAC C
12333550 TGACCCGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.35, C:0.52, G:0.13, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:12334196 original size:21 final size:21
Alignment explanation
Indices: 12334170--12334419 Score: 105
Period size: 21 Copynumber: 12.0 Consensus size: 21
12334160 GCAATTTTGA
*
12334170 ACTATCGCAATGCGATAGTCG
1 ACTATCGCATTGCGATAGTCG
* * *
12334191 ACTATCGCAATGCGA-ACTTGG
1 ACTATCGCATTGCGATA-GTCG
*
12334212 ACTATTGCATTGCGATAGTCG
1 ACTATCGCATTGCGATAGTCG
* *
12334233 ACTATCACATTGCGATTAAT-G
1 ACTATCGCATTGCGA-TAGTCG
* * *
12334254 TA-AATCGCAATGCGATAGTCCA
1 -ACTATCGCATTGCGATAGT-CG
* * *
12334276 AGT-TCGCATTACGATTGTCG
1 ACTATCGCATTGCGATAGTCG
*
12334296 ACTATCGCATTGCGAT--T-T
1 ACTATCGCATTGCGATAGTCG
*
12334314 ACATATTCGCATTGCGAT--T-T
1 AC-TA-TCGCATTGCGATAGTCG
**
12334334 ACATATTCGCATTGCGAT--TTT
1 AC-TA-TCGCATTGCGATAGTCG
*
12334355 ACATATTCGCATTGCGATAGTCA
1 AC-TA-TCGCATTGCGATAGTCG
* *
12334378 AGT-TCGCATTGCGATAGTCCA
1 ACTATCGCATTGCGATAGT-CG
* *
12334399 AGT-TCGCGTTGCGATAGTCG
1 ACTATCGCATTGCGATAGTCG
12334419 A
1 A
12334420 AGTTCGCGTT
Statistics
Matches: 188, Mismatches: 27, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
18 2 0.01
19 3 0.02
20 57 0.30
21 118 0.63
22 6 0.03
23 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
ACTATCGCATTGCGATAGTCG
Done.