Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009352.1 Hibiscus syriacus cultivar Beakdansim tig00113156_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: 624088
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:2645 original size:20 final size:20
Alignment explanation
Indices: 2608--2645 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2598 CTACTCTTCA
*
2608 TTTTCATTTTTTTGTTTTCT
1 TTTTCATTTTTTTCTTTTCT
2628 TTTTC-TTTTGTTTCTTTT
1 TTTTCATTTT-TTTCTTTT
2646 AGGCCATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.03, C:0.11, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTCATTTTTTTCTTTTCT
Found at i:3753 original size:2 final size:2
Alignment explanation
Indices: 3746--3776 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3736 CAGCATTATT
3746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3777 TTAAAGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5655 original size:19 final size:19
Alignment explanation
Indices: 5611--5655 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5601 TTTTAAAAAT
* *
5611 ATTTTTAGTAAAAAGTTAG
1 ATTTTTTGTAAAAAATTAG
5630 ATTTTTTGTAAATAAATTA-
1 ATTTTTTGTAAA-AAATTAG
5649 ATTTTTT
1 ATTTTTT
5656 TTAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (19 bp):
ATTTTTTGTAAAAAATTAG
Found at i:6676 original size:14 final size:15
Alignment explanation
Indices: 6657--6690 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6647 TTTTAAAAAA
6657 TAAATTATTT-AATT
1 TAAATTATTTAAATT
6671 TAAATTATTTCAAATT
1 TAAATTATTT-AAATT
6687 TAAA
1 TAAA
6691 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTATTTAAATT
Found at i:13154 original size:11 final size:11
Alignment explanation
Indices: 13134--13174 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
13124 ATAAAAAATA
*
13134 AAAAAATATAT
1 AAAAATTATAT
13145 AAAAATTATA-
1 AAAAATTATAT
*
13155 AATAA-TATAT
1 AAAAATTATAT
13165 AAAAATTATA
1 AAAAATTATA
13175 AATAATAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 4 0.16
10 8 0.32
11 13 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:13161 original size:20 final size:20
Alignment explanation
Indices: 13119--13181 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
13109 CATATTTTCA
* * *
13119 AATAAATAAAAAATA-AAAA
1 AATATATAAAAATTATAAAT
13138 AATATATAAAAATTATAAAT
1 AATATATAAAAATTATAAAT
13158 AATATATAAAAATTATAAAT
1 AATATATAAAAATTATAAAT
13178 AATA
1 AATA
13182 GAAACTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATATATAAAAATTATAAAT
Found at i:13174 original size:9 final size:9
Alignment explanation
Indices: 13124--13176 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
13114 TTTCAAATAA
*
13124 ATAAAAAAT
1 ATAAAAATT
*
13133 AAAAAAATAT
1 ATAAAAAT-T
13143 ATAAAAATT
1 ATAAAAATT
13152 ATAAATAATAT
1 ATAAA-AAT-T
13163 ATAAAAATT
1 ATAAAAATT
13172 ATAAA
1 ATAAA
13177 TAATAGAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
9 18 0.47
10 14 0.37
11 6 0.16
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
ATAAAAATT
Found at i:18571 original size:4 final size:4
Alignment explanation
Indices: 18562--18588 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18552 TGGACTACAG
18562 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
18589 AGCACCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:22735 original size:15 final size:15
Alignment explanation
Indices: 22709--22745 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
22699 TAATATACAT
22709 ATATTATTCAAAAATA
1 ATATT-TTCAAAAATA
22725 ATATTTTCAAAAATA
1 ATATTTTCAAAAATA
22740 ATATTT
1 ATATTT
22746 GTTCATGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTTCAAAAATA
Found at i:24962 original size:17 final size:17
Alignment explanation
Indices: 24940--24986 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
24930 TTAAATAAAT
24940 TAAAAATATTATATTTA
1 TAAAAATATTATATTTA
*
24957 TAAAAACTA-TATTTTTA
1 TAAAAA-TATTATATTTA
* *
24974 TAATATTATTATA
1 TAAAAATATTATA
24987 AAAAAGGCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAAATATTATATTTA
Found at i:26356 original size:35 final size:35
Alignment explanation
Indices: 26316--26393 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
26306 TCATCAATTC
* * **
26316 ATTCTAAACCCCAATTTCCAAAGTAATTCAATTTT
1 ATTCTAAACCCCAAATTCCAAAATAATTCAATTAA
* * *
26351 ATTCTAAACCCTAAATTCTAAAATACTTCAATTAA
1 ATTCTAAACCCCAAATTCCAAAATAATTCAATTAA
26386 ATTCTAAA
1 ATTCTAAA
26394 ATACTTCAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
ATTCTAAACCCCAAATTCCAAAATAATTCAATTAA
Found at i:26387 original size:21 final size:21
Alignment explanation
Indices: 26362--26404 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
26352 TTCTAAACCC
26362 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
26383 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
26404 T
1 T
26405 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:27226 original size:130 final size:128
Alignment explanation
Indices: 27008--27253 Score: 420
Period size: 130 Copynumber: 1.9 Consensus size: 128
26998 AATTTTCTTC
*
27008 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTTAACACATGTCAGATCC
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTTAACACATGTCAGATCC
*
27073 TGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
27136 TAATTAGGTGGTAACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGT--TAACACATGTCAGAT
27201 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
64 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
27254 TATATAAATA
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
128 43 0.39
130 67 0.61
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (128 bp):
TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTTAACACATGTCAGATCC
TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:27904 original size:29 final size:29
Alignment explanation
Indices: 27852--27911 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
27842 GCAAACGGAA
* * *
27852 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGCTT
27881 TAAATGTTGGGGGACCT-AAATGCAAGCTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGCTT
27910 TA
1 TA
27912 GAAATGTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.33
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGCTT
Found at i:32780 original size:51 final size:51
Alignment explanation
Indices: 32706--32966 Score: 299
Period size: 51 Copynumber: 5.1 Consensus size: 51
32696 AAATCTTCAG
* *
32706 CAAACGAGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTT
* ** * * *
32757 CGATTGAGTTCGCTCCCTT-TTTCTTTAGGGAGTATAGAACTCAAAAATCTTCTT
1 CAAACGGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTCGAAAA---TCTT
** * * *
32811 CTTACGGGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTT
** * *
32862 CAAACGGGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTT
* * *
32913 CAAACGGGTTCGCTCCTTCTTTCATTAAGGAGAATAGAACTCGAATATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTT
32964 CAA
1 CAA
32967 CAATCGTGTC
Statistics
Matches: 178, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
51 134 0.75
52 4 0.02
53 3 0.02
54 37 0.21
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTT
Found at i:32876 original size:105 final size:102
Alignment explanation
Indices: 32706--32966 Score: 299
Period size: 105 Copynumber: 2.5 Consensus size: 102
32696 AAATCTTCAG
* * * **
32706 CAAACGAGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCGATTGAGTTCGCT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCAAACGAGTTCGCT
** ** *
32771 CCCTT-TTTCTTTAGGGAGTATAGAACTCAAAAATCTTCTT
66 -CCTTCTCACTTTAAAGAGTATAGAACTC--AAA-CATCTT
** * * * *
32811 CTTACGGGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCAAACGAGTTCGCT
*
32876 CCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTT
66 CCTTCTCACTTTAAAGAGTATAGAACTCAAACATCTT
* * *
32913 CAAACGGGTTCGCTCCTTCTTTCATTAAGGAGAATAGAACTCGAATATCTTCAA
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCAA
32967 CAATCGTGTC
Statistics
Matches: 130, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
102 51 0.39
103 2 0.02
104 4 0.03
105 73 0.56
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (102 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCAAACGAGTTCGCT
CCTTCTCACTTTAAAGAGTATAGAACTCAAACATCTT
Found at i:32999 original size:156 final size:156
Alignment explanation
Indices: 32706--33010 Score: 339
Period size: 156 Copynumber: 2.0 Consensus size: 156
32696 AAATCTTCAG
** * * **
32706 CAAACGAGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCGATTGAGTTCGCT
1 CAAACGAGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTCAAACGAGTTCGCT
* * * ** * * *
32771 CCCTTTTTCTTTAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCATTCTCTCTT
66 CCCTTTTTCATTAAGGAGAATAGAACTCAAAAATCTTCAACATACGGGTTCGCTCACTATCTCTT
*
32836 TAAAGAGTAT-AGAACTCGAAAATCTT
131 CAAAGAGTATGAG-ACTCGAAAATCTT
* *
32862 CAAACGGGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
1 CAAACGAGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTCAAACGAGTTCGCT
* * * * *
32927 -CCTTCTTTCATTAAGGAGAATAGAACTCGAATATCTTCAACA-ATCGTG-TCTGCTCCCTATTT
66 CCCTT-TTTCATTAAGGAGAATAGAACTCAAAAATCTTCAACATA-CGGGTTC-GCTCACTATCT
*
32989 CTTCAGAGAGTATGAGACTCGA
128 CTTCAAAGAGTATGAGACTCGA
33011 TCAATTTTCA
Statistics
Matches: 122, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
155 7 0.06
156 113 0.93
157 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (156 bp):
CAAACGAGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTCAAACGAGTTCGCT
CCCTTTTTCATTAAGGAGAATAGAACTCAAAAATCTTCAACATACGGGTTCGCTCACTATCTCTT
CAAAGAGTATGAGACTCGAAAATCTT
Found at i:33027 original size:55 final size:55
Alignment explanation
Indices: 32959--33130 Score: 290
Period size: 55 Copynumber: 3.1 Consensus size: 55
32949 GAACTCGAAT
*
32959 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGATCA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCA
* * *
33014 ATTTTCAACAATCGTGTCTGCTCCCTATTTTTTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTA-TTTCTTCAGAGAGTATAAGACTCGATCA
*
33070 ATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCA
33125 ATCTTC
1 ATCTTC
33131 GATTATCGTT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
55 58 0.54
56 50 0.46
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (55 bp):
ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCA
Found at i:37651 original size:8 final size:8
Alignment explanation
Indices: 37638--37665 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
37628 GAAAAAGAAG
37638 ATATATAC
1 ATATATAC
37646 ATATATAC
1 ATATATAC
37654 ATATATAC
1 ATATATAC
37662 ATAT
1 ATAT
37666 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:48149 original size:3 final size:3
Alignment explanation
Indices: 48141--48181 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
48131 ATACATGTTC
48141 ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48182 TAAATGACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:61473 original size:42 final size:44
Alignment explanation
Indices: 61421--61504 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 44
61411 AAGAATAAAG
*
61421 ACTCTTTTTC-TTGTCAC-AAGTTCCTAAAGAGTTGGTAAAGAC
1 ACTCTTTTTCTTTGTCACAAAGTTACTAAAGAGTTGGTAAAGAC
*
61463 ACTCTTTTTCTTTGTCACAGAAGTTACTAAAGTGTTGGTAAA
1 ACTCTTTTTCTTTGTCACA-AAGTTACTAAAGAGTTGGTAAA
61505 TGATATACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 10 0.27
43 7 0.19
45 20 0.54
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (44 bp):
ACTCTTTTTCTTTGTCACAAAGTTACTAAAGAGTTGGTAAAGAC
Found at i:62345 original size:2 final size:2
Alignment explanation
Indices: 62338--62390 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
62328 TCCTCTGGAT
62338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62380 TA TA TA TA TA T
1 TA TA TA TA TA T
62391 TCAACTAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67273 original size:37 final size:33
Alignment explanation
Indices: 67231--67313 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 33
67221 TAAAATTATA
67231 TTTAAAATTTATTTTTGTTTCATTTTAGTATCTTG
1 TTTAAAATTTA-TTTT-TTTCATTTTAGTATCTTG
*
67266 TAGTTAAAAACGTTATTTTTTTCATTTTAGTATCTTG
1 T--TT-AAAA-TTTATTTTTTTCATTTTAGTATCTTG
67303 TTTAAAATTTA
1 TTTAAAATTTA
67314 ACTTAGGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
33 3 0.07
34 4 0.10
35 3 0.07
37 21 0.50
38 8 0.19
39 3 0.07
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (33 bp):
TTTAAAATTTATTTTTTTCATTTTAGTATCTTG
Found at i:100606 original size:22 final size:22
Alignment explanation
Indices: 100578--100623 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
100568 ATATTTTGAT
100578 TAAAAATATATAAATA-ATTAAA
1 TAAAAATATA-AAATATATTAAA
*
100600 TAAAAATATAATATATATTAAA
1 TAAAAATATAAAATATATTAAA
100622 TA
1 TA
100624 CTTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAATATAAAATATATTAAA
Found at i:114682 original size:32 final size:32
Alignment explanation
Indices: 114610--114671 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
114600 GGTGTTTTAG
*
114610 CACATGTCACGTCATCATTTTAGATGAGATAA
1 CACATGTCACGTCATCATTTTAGATGACATAA
* *
114642 CACATGTCACGTCATTATTTTAGGTGACAT
1 CACATGTCACGTCATCATTTTAGATGACAT
114672 GGAACATGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (32 bp):
CACATGTCACGTCATCATTTTAGATGACATAA
Found at i:118467 original size:21 final size:22
Alignment explanation
Indices: 118443--118488 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
118433 GAAAAAATCA
*
118443 GATATCCGAAAT-TTCGGAT-CG
1 GATATCC-AAATATCCGGATCCG
118464 GATATCCAAATATCCGGATCCG
1 GATATCCAAATATCCGGATCCG
118486 GAT
1 GAT
118489 CTGAATCCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
GATATCCAAATATCCGGATCCG
Found at i:122159 original size:58 final size:58
Alignment explanation
Indices: 122061--122171 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
122051 AAATATAACC
* * * *
122061 CTCATTTTAATTTAGTTCCTAAACTTTTGAATATTATAATTTCATCCCTAAACCGACT
1 CTCATTCTAAATTAGTTCCTAAACTTTTGAACATCATAATTTCATCCCTAAACCGACT
* *
122119 CTCATTCTAAATTAG-TCCTTAAACTTTTGAACATCCTAATTTCATCTCTAAAC
1 CTCATTCTAAATTAGTTCC-TAAACTTTTGAACATCATAATTTCATCCCTAAAC
122172 TATGAACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.07
58 43 0.93
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (58 bp):
CTCATTCTAAATTAGTTCCTAAACTTTTGAACATCATAATTTCATCCCTAAACCGACT
Found at i:129392 original size:291 final size:292
Alignment explanation
Indices: 128868--129451 Score: 1161
Period size: 291 Copynumber: 2.0 Consensus size: 292
128858 CACCTCGATC
128868 CCTTTCCGGCAAGGTGCATTCGATCAAGTGCATGCCTAGTGCACCTAGGTGCAATTTTTTGTAAG
1 CCTTTCCGGCAAGGTGCATTCGATCAAGTGCATGCCTAGTGCACCTAGGTGCAATTTTTTGTAAG
128933 GTGATGGACGTAAAAGAAAAGGCCCACCTCTCTGAAGTTTATTATATATCTTAAAGCTTTAAATG
66 GTGATGGACGTAAAAGAAAAGGCCCACCTCTCTGAAGTTTATTATATATCTTAAAGCTTTAAATG
128998 CATGCGCGGACGCACACAGGCAAACACTCCTTTAATGCCTCAAGGGAAATACAAGGGTTCTAGCG
131 CATGCGCGGACGCACACAGGCAAACACTCCTTTAATGCCTCAAGGGAAATACAAGGGTTCTAGCG
129063 GCTAAAGTGTGGCTTTGTCCCCTTTACAACACTGAATTTTAGAGAATCACAACTTGCTTAGTTCG
196 GCTAAAGTGTGGCTTTGTCCCCTTTACAACACTGAATTTTAGAGAATCACAACTTGCTTAGTTCG
129128 TTGAAATCCTAGGATCATTC-AAAGAGACGGT
261 TTGAAATCCTAGGATCATTCAAAAGAGACGGT
129159 CCTTTCCGGCAAGGTGCATTCGATCAAGTGCATGCCTAGTGCACCTAGGTGCAATTTTTTGTAAG
1 CCTTTCCGGCAAGGTGCATTCGATCAAGTGCATGCCTAGTGCACCTAGGTGCAATTTTTTGTAAG
129224 GTGATGGACGTAAAAGAAAAGGCCCACCTCTCTGAAGTTTATTATATATCTTAAAGCTTTAAATG
66 GTGATGGACGTAAAAGAAAAGGCCCACCTCTCTGAAGTTTATTATATATCTTAAAGCTTTAAATG
129289 CATGCGCGGACGCACACAGGCAAACACTCCTTTAATGCCTCAAGGGAAATACAAGGGTTCTAGCG
131 CATGCGCGGACGCACACAGGCAAACACTCCTTTAATGCCTCAAGGGAAATACAAGGGTTCTAGCG
129354 GCTAAAGTGTGGCTTTGTCCCCTTTACAACACTGAATTTTAGAGAATCACAACTTGCTTAGTTCG
196 GCTAAAGTGTGGCTTTGTCCCCTTTACAACACTGAATTTTAGAGAATCACAACTTGCTTAGTTCG
129419 TTGAAATCCTAGGATCATTCAAAAGAGACGGT
261 TTGAAATCCTAGGATCATTCAAAAGAGACGGT
129451 C
1 C
129452 AGATTAAAGG
Statistics
Matches: 292, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
291 280 0.96
292 12 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (292 bp):
CCTTTCCGGCAAGGTGCATTCGATCAAGTGCATGCCTAGTGCACCTAGGTGCAATTTTTTGTAAG
GTGATGGACGTAAAAGAAAAGGCCCACCTCTCTGAAGTTTATTATATATCTTAAAGCTTTAAATG
CATGCGCGGACGCACACAGGCAAACACTCCTTTAATGCCTCAAGGGAAATACAAGGGTTCTAGCG
GCTAAAGTGTGGCTTTGTCCCCTTTACAACACTGAATTTTAGAGAATCACAACTTGCTTAGTTCG
TTGAAATCCTAGGATCATTCAAAAGAGACGGT
Found at i:144113 original size:18 final size:19
Alignment explanation
Indices: 144078--144114 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
144068 ATGGGAATGC
144078 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
144098 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
144115 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:144333 original size:37 final size:36
Alignment explanation
Indices: 144261--144334 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
144251 GTTGGAAAAT
*
144261 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
* *
144297 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAATCATAAA
144334 A
1 A
144335 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 21 0.64
38 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:149676 original size:2 final size:2
Alignment explanation
Indices: 149671--149707 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
149661 AATACATCAA
149671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149708 TATTTGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:160335 original size:2 final size:2
Alignment explanation
Indices: 160328--160375 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
160318 AAAATAAACA
*
160328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160370 AT AT AT
1 AT AT AT
160376 GAAAATGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:160521 original size:2 final size:2
Alignment explanation
Indices: 160514--160559 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
160504 AAAAATAAAC
160514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160556 AT AT
1 AT AT
160560 TGAGACAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160557 original size:188 final size:191
Alignment explanation
Indices: 160184--160559 Score: 699
Period size: 191 Copynumber: 2.0 Consensus size: 191
160174 TTTTTTAATA
160184 GAAAATGATGAGTTTGGAACACAATGATTAGTCAGGTGACCATTTTATAACTTGTGATAGCTGGA
1 GAAAATGATGAGTTTGGAACACAATGATTAGTCAGGTGACCATTTTATAACTTGTGATAGCTGGA
160249 GGACTCAATAAAATAACATCCTATAGTCGGGGACCATTTATGTACTTTACCCTTTTTAGTTATAC
66 GGACTCAAT-AAATAACATCCTATAGTCGGGGACCATTTATGTACTTTACCCTTTTTAGTTATAC
160314 TATAAAAATAAACAATATATATATATATATATATATATATATATAGATATATATATATATAT
130 TATAAAAATAAACAATATATATATATATATATATATATATATATAGATATATATATATATAT
160376 GAAAATGATGAG-TTGGAACACAATGATTAGTCAGGTGACCATTTTATAACTTGTGATAGCTGGA
1 GAAAATGATGAGTTTGGAACACAATGATTAGTCAGGTGACCATTTTATAACTTGTGATAGCTGGA
160440 GGACTCAAT-AA-AACATCCTATAGTCGGGGACCA-TTATGTACTTTACCCTTTTTAGTTATACT
66 GGACTCAATAAATAACATCCTATAGTCGGGGACCATTTATGTACTTTACCCTTTTTAGTTATACT
*
160502 ATAAAAATAAAC-ATATATATATATATATATATATATATATATATATATATATATATAT
131 ATAAAAATAAACAATATATATATATATATATATATATATATATAGATATATATATATAT
160560 TGAGACAATG
Statistics
Matches: 183, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
186 45 0.25
187 41 0.22
188 22 0.12
189 2 0.01
191 61 0.33
192 12 0.07
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (191 bp):
GAAAATGATGAGTTTGGAACACAATGATTAGTCAGGTGACCATTTTATAACTTGTGATAGCTGGA
GGACTCAATAAATAACATCCTATAGTCGGGGACCATTTATGTACTTTACCCTTTTTAGTTATACT
ATAAAAATAAACAATATATATATATATATATATATATATATATAGATATATATATATATAT
Found at i:165741 original size:2 final size:2
Alignment explanation
Indices: 165736--165764 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
165726 ACACACGCGC
165736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
165765 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:167639 original size:2 final size:2
Alignment explanation
Indices: 167632--167657 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
167622 TCCCCTACCC
167632 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
167658 GGGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:170027 original size:16 final size:17
Alignment explanation
Indices: 169986--170027 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
169976 GAGTGTGAGC
169986 ATTTAAAAAAATTATAA
1 ATTTAAAAAAATTATAA
*
170003 A-TTAAAAAAAATA-AA
1 ATTTAAAAAAATTATAA
*
170018 ATTTATAAAA
1 ATTTAAAAAA
170028 GTCATTGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTTAAAAAAATTATAA
Found at i:170835 original size:23 final size:23
Alignment explanation
Indices: 170792--170835 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
170782 ACCAAAAGGA
* * *
170792 AGAGAAAAATATGTCATAAAGAC
1 AGAGAAAAACATGCCACAAAGAC
170815 AGAGAAAAACATGCCACAAAG
1 AGAGAAAAACATGCCACAAAG
170836 CATAGCCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.14, G:0.18, T:0.11
Consensus pattern (23 bp):
AGAGAAAAACATGCCACAAAGAC
Found at i:174621 original size:24 final size:23
Alignment explanation
Indices: 174575--174617 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
174565 GTTATATTTT
*
174575 TTATTTTTATAATAATAAAAATA
1 TTATTTTTAAAATAATAAAAATA
*
174598 TTATTTTTAAAA-ATTAAAAA
1 TTATTTTTAAAATAATAAAAA
174618 AATAATCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATTTTTAAAATAATAAAAATA
Found at i:180870 original size:26 final size:23
Alignment explanation
Indices: 180841--180894 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
180831 AATTATTAAT
180841 TTAATCTTGAAATTTAGAAAGAAATA
1 TTAAT-TTGAAA--TAGAAAGAAATA
*
180867 TTAA-TTGAAATAGAAAGAAGTA
1 TTAATTTGAAATAGAAAGAAATA
180889 TTAATT
1 TTAATT
180895 GAACTTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 15 0.58
23 1 0.04
24 6 0.23
26 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (23 bp):
TTAATTTGAAATAGAAAGAAATA
Found at i:180883 original size:22 final size:22
Alignment explanation
Indices: 180855--180897 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
180845 TCTTGAAATT
180855 TAGAAAGAAATATTAATTGAAA
1 TAGAAAGAAATATTAATTGAAA
*
180877 TAGAAAGAAGTATTAATTGAA
1 TAGAAAGAAATATTAATTGAA
180898 CTTATGACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (22 bp):
TAGAAAGAAATATTAATTGAAA
Found at i:185740 original size:14 final size:14
Alignment explanation
Indices: 185706--185743 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
185696 AAACACAAAT
185706 TCTAAATC-TACAC
1 TCTAAATCATACAC
* *
185719 TTTAAATCATACCC
1 TCTAAATCATACAC
185733 TCTAAATCATA
1 TCTAAATCATA
185744 AACTATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (14 bp):
TCTAAATCATACAC
Found at i:186972 original size:23 final size:23
Alignment explanation
Indices: 186946--186989 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
186936 TCTCGATTCG
*
186946 TTGTTTGTATTGCTCGTGTTTGA
1 TTGTTTGTATTGCTCGAGTTTGA
186969 TTGTTTGTATTGCTCGAGTTT
1 TTGTTTGTATTGCTCGAGTTT
186990 TCCTTCTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.25, T:0.57
Consensus pattern (23 bp):
TTGTTTGTATTGCTCGAGTTTGA
Found at i:187995 original size:20 final size:19
Alignment explanation
Indices: 187935--187995 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
187925 TATTAGGAAA
*
187935 AAAATCTTAAATATAAT-AT
1 AAAATATTAAA-ATAATAAT
*
187954 ATAAATAATAAAATAA-ACAT
1 A-AAATATTAAAATAATA-AT
187974 AAAAGTATTAAAATAATAAT
1 AAAA-TATTAAAATAATAAT
187994 AA
1 AA
187996 TTATCCCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 8 0.24
20 25 0.74
21 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATATTAAAATAATAAT
Found at i:190198 original size:6 final size:6
Alignment explanation
Indices: 190189--190217 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
190179 ATATAATTAT
190189 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
190218 TATGTATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:221533 original size:24 final size:24
Alignment explanation
Indices: 221479--221533 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
221469 GCTGACTTCC
*
221479 GCAGCTGTCGCAATAGCAGCAGCA
1 GCAGCTGTAGCAATAGCAGCAGCA
* * *
221503 GCTGCTGTAGCAA-AGGCTGCAGCT
1 GCAGCTGTAGCAATA-GCAGCAGCA
221527 GCAGCTG
1 GCAGCTG
221534 CCATGTTGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.16
Consensus pattern (24 bp):
GCAGCTGTAGCAATAGCAGCAGCA
Found at i:225502 original size:31 final size:32
Alignment explanation
Indices: 225443--225505 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
225433 CCGTTCTTAA
* *
225443 CTATTTTAATATGTTTTGAAATATAATATTTT
1 CTATTTCAATATGTTTTGAAATAAAATATTTT
*
225475 CTATTTCAATATG-TTTGAATTAAAATATTTT
1 CTATTTCAATATGTTTTGAAATAAAATATTTT
225506 GAAATATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (32 bp):
CTATTTCAATATGTTTTGAAATAAAATATTTT
Found at i:227369 original size:31 final size:31
Alignment explanation
Indices: 227329--227405 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
227319 ATTTTTAAAT
* *
227329 GATTTTTAAATTTTTTAA-ATTATTAT-AAAA
1 GATTATTAAATTTATTAACA-TATTATAAAAA
227359 GATTCATTAAATTTATTAACATATTATAAAAA
1 GATT-ATTAAATTTATTAACATATTATAAAAA
*
227391 GATTATTAAACTTAT
1 GATTATTAAATTTAT
227406 CAAAATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.10
31 28 0.68
32 9 0.22
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (31 bp):
GATTATTAAATTTATTAACATATTATAAAAA
Found at i:241737 original size:23 final size:22
Alignment explanation
Indices: 241698--241744 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
241688 TTTTGTATTA
*
241698 TTAAAAATTAAAAAATTTAATT
1 TTAAAAATTAAAAAATTCAATT
**
241720 TTAAAATATTAATTAATTCAATT
1 TTAAAA-ATTAAAAAATTCAATT
241743 TT
1 TT
241745 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAAATTAAAAAATTCAATT
Found at i:242935 original size:25 final size:26
Alignment explanation
Indices: 242874--242938 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
242864 TTAAATTCAT
242874 AATATTTTTTATATATTAACTTTAAGA
1 AATATTTTTT-TATATTAACTTTAAGA
* * **
242901 AATATGTTTTTGTATTAAC-TTATTA
1 AATATTTTTTTATATTAACTTTAAGA
242926 AATATTTTTTTAT
1 AATATTTTTTTAT
242939 TAACCTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 15 0.47
26 8 0.25
27 9 0.28
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (26 bp):
AATATTTTTTTATATTAACTTTAAGA
Found at i:242952 original size:25 final size:25
Alignment explanation
Indices: 242900--242948 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
242890 TAACTTTAAG
*
242900 AAATATGTTTTTGTATTAACTTATT
1 AAATATGTTTTTGTATTAACTAATT
242925 AAATAT-TTTTT-TATTAACCTAATT
1 AAATATGTTTTTGTATTAA-CTAATT
242949 TAAAAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 10 0.45
25 6 0.27
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (25 bp):
AAATATGTTTTTGTATTAACTAATT
Found at i:243374 original size:2 final size:2
Alignment explanation
Indices: 243367--243398 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
243357 AACTGAGCCA
243367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
243399 TTGCAACGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244953 original size:23 final size:23
Alignment explanation
Indices: 244909--244953 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
244899 ACTTAAATCA
*
244909 TTAAAATTAATCTAATAGTTTAT
1 TTAAAATTAATCTAAGAGTTTAT
* * *
244932 TTAAAATTGATTTAAGATTTTA
1 TTAAAATTAATCTAAGAGTTTA
244954 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (23 bp):
TTAAAATTAATCTAAGAGTTTAT
Found at i:245048 original size:14 final size:15
Alignment explanation
Indices: 245023--245095 Score: 53
Period size: 17 Copynumber: 4.7 Consensus size: 15
245013 ATCATTAAAA
245023 ATAATT-TAATATTC
1 ATAATTATAATATTC
*
245037 A-AATTATAATATAC
1 ATAATTATAATATTC
* *
245051 ATTATATTATAATTAATG
1 A-TA-ATTATAA-TATTC
245069 ATATATATATAATATTC
1 ATA-AT-TATAATATTC
245086 A-AATTATAAT
1 ATAATTATAAT
245096 CATACATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
13 4 0.09
14 15 0.32
15 2 0.04
16 2 0.04
17 16 0.34
18 8 0.17
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (15 bp):
ATAATTATAATATTC
Found at i:245090 original size:26 final size:24
Alignment explanation
Indices: 245029--245102 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 24
245019 AAAAATAATT
245029 TAATATTCAAATT-ATAATATACA
1 TAATATTCAAATTAATAATATACA
* *
245052 TTATATT-ATAATTAATGATATATATA
1 TAATATTCA-AATTAAT-A-ATATACA
245078 TAATATTCAAATT-ATAATCATACA
1 TAATATTCAAATTAATAAT-ATACA
245102 T
1 T
245103 TTGTAACATG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 1 0.02
23 12 0.29
24 8 0.20
25 3 0.07
26 16 0.39
27 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (24 bp):
TAATATTCAAATTAATAATATACA
Found at i:246744 original size:5 final size:5
Alignment explanation
Indices: 246734--246760 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
246724 TATCAAAAAT
246734 TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
246761 TAAATCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:253226 original size:17 final size:16
Alignment explanation
Indices: 253200--253252 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
253190 TTATACAAAA
*
253200 AAGTATTTAAATCATTT
1 AAGTACTTAAAT-ATTT
253217 AAGTACTTAAAATATTT
1 AAGTACTT-AAATATTT
*
253234 AAGTACTTATATGATTT
1 AAGTACTTAAAT-ATTT
253251 AA
1 AA
253253 ATATTTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.09
17 25 0.78
18 4 0.12
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (16 bp):
AAGTACTTAAATATTT
Found at i:253260 original size:25 final size:25
Alignment explanation
Indices: 253226--253283 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
253216 TAAGTACTTA
253226 AAATATTTAAGTACTTATATGATTT
1 AAATATTTAAGTACTTATATGATTT
253251 AAATATTTAAGTACTTATATGATTT
1 AAATATTTAAGTACTTATATGATTT
253276 AAATATTT
1 AAATATTT
253284 TTTATAGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (25 bp):
AAATATTTAAGTACTTATATGATTT
Found at i:253302 original size:16 final size:16
Alignment explanation
Indices: 253276--253312 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
253266 TATATGATTT
253276 AAATA-TTTTTTATAG
1 AAATATTTTTTTATAG
*
253291 ACATATTTTTTTATAG
1 AAATATTTTTTTATAG
253307 AAATAT
1 AAATAT
253313 GGGTCTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (16 bp):
AAATATTTTTTTATAG
Found at i:255407 original size:21 final size:21
Alignment explanation
Indices: 255381--255433 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
255371 CATCCATGTT
255381 ATCAACTATCATGAACGTCAC
1 ATCAACTATCATGAACGTCAC
* *
255402 ATCAACTATAATGGACGTCAC
1 ATCAACTATCATGAACGTCAC
255423 ATCAACTATCA
1 ATCAACTATCA
255434 CGTCAGCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25
Consensus pattern (21 bp):
ATCAACTATCATGAACGTCAC
Found at i:258075 original size:16 final size:16
Alignment explanation
Indices: 258054--258086 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
258044 GATTAAGCGA
258054 TGAATGATTCAAATGC
1 TGAATGATTCAAATGC
258070 TGAATGATTCAAATGC
1 TGAATGATTCAAATGC
258086 T
1 T
258087 CTGTATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (16 bp):
TGAATGATTCAAATGC
Found at i:261016 original size:22 final size:21
Alignment explanation
Indices: 260970--261016 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
260960 AAAAAGGTCA
*
260970 AATT-TTTTAAATTTTGACAT
1 AATTATTTTAAATTTTGAAAT
* *
260990 GATTATTTTAAATATTTTAAAT
1 AATTATTTTAAAT-TTTGAAAT
261012 AATTA
1 AATTA
261017 AAATTTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
AATTATTTTAAATTTTGAAAT
Found at i:263374 original size:20 final size:20
Alignment explanation
Indices: 263330--263375 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
263320 TTGTGCAAAG
* *
263330 TCATTTAATAAATTTAATGA
1 TCATTTTATAAATGTAATGA
263350 T-ATTTTATAAGATGTAAT-A
1 TCATTTTATAA-ATGTAATGA
263369 TCATTTT
1 TCATTTT
263376 TAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (20 bp):
TCATTTTATAAATGTAATGA
Found at i:275375 original size:23 final size:22
Alignment explanation
Indices: 275345--275390 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
275335 CAATGAAACG
275345 TTGGATGAATATGGATGCTTTTT
1 TTGGATGAATATGGATG-TTTTT
*
275368 TTGGATGAATTTGGATGTTTTT
1 TTGGATGAATATGGATGTTTTT
275390 T
1 T
275391 CAGGTGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.20, C:0.02, G:0.26, T:0.52
Consensus pattern (22 bp):
TTGGATGAATATGGATGTTTTT
Found at i:277454 original size:21 final size:21
Alignment explanation
Indices: 277429--277471 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
277419 ATTCAAAGAG
*
277429 TTTGACTGATAAAATGACACT
1 TTTGACTGATAAAATGAAACT
277450 TTTGACTGATAAAATGAAACT
1 TTTGACTGATAAAATGAAACT
277471 T
1 T
277472 CTAAACTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTGACTGATAAAATGAAACT
Found at i:278496 original size:57 final size:58
Alignment explanation
Indices: 278356--278499 Score: 195
Period size: 57 Copynumber: 2.5 Consensus size: 58
278346 GTAAAGATAT
* *
278356 GATAAGGTGACATGAATATAA-ATATAATCTTATTCATATTTGATGATACGAAAATAA
1 GATAAGGTGACATGAATATAAGATATGATCTTATTCATATTTGATGATACAAAAATAA
* **
278413 GATAAGGTGACATGATTATGTGATATGATC-TATTCATATTTTG-TGATACAAAAATAA
1 GATAAGGTGACATGAATATAAGATATGATCTTATTCATA-TTTGATGATACAAAAATAA
* *
278470 GATAAAGTGACGTGAATATAAGATATGATC
1 GATAAGGTGACATGAATATAAGATATGATC
278500 AAGTGACTCG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
57 64 0.85
58 11 0.15
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.33
Consensus pattern (58 bp):
GATAAGGTGACATGAATATAAGATATGATCTTATTCATATTTGATGATACAAAAATAA
Found at i:280962 original size:15 final size:15
Alignment explanation
Indices: 280942--280980 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
280932 GTTTACTTCA
*
280942 GAATGATTAAGCGCT
1 GAATGATTAAACGCT
*
280957 GAATGATTTAAATGCT
1 GAATGA-TTAAACGCT
280973 GAATGATT
1 GAATGATT
280981 CAGAGACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (15 bp):
GAATGATTAAACGCT
Found at i:284338 original size:4 final size:4
Alignment explanation
Indices: 284329--284376 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
284319 AGTTCTCTGG
284329 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
284377 CTCTCTCTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:288570 original size:20 final size:20
Alignment explanation
Indices: 288545--288596 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
288535 ATCCAAGGGC
288545 TAAATTCCAAATTTATATTA
1 TAAATTCCAAATTTATATTA
288565 TAAATTCCAAATTTATATTA
1 TAAATTCCAAATTTATATTA
288585 TAAATTCCAAAT
1 TAAATTCCAAAT
288597 AAAGTAACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTCCAAATTTATATTA
Found at i:291751 original size:20 final size:20
Alignment explanation
Indices: 291726--291770 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
291716 TTTTATCCGA
*
291726 AAAAATCCGGTATGGGGTTT
1 AAAAATCCGGTATGAGGTTT
*
291746 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTATGAGGTTT
291766 AAAAA
1 AAAAA
291771 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTATGAGGTTT
Found at i:312047 original size:18 final size:19
Alignment explanation
Indices: 312012--312052 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
312002 GATTTTTGGT
*
312012 TTTTATTTTTTTACTTT-C
1 TTTTATTATTTTACTTTCC
312030 TTTTATTATTTT-CTTTTCC
1 TTTTATTATTTTAC-TTTCC
312049 TTTT
1 TTTT
312053 CTGTGTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.70
19 5 0.25
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTATTTTACTTTCC
Found at i:321842 original size:17 final size:17
Alignment explanation
Indices: 321820--321853 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
321810 TTACTTATTG
321820 CTTGGATCTCTTTTCAC
1 CTTGGATCTCTTTTCAC
321837 CTTGGATCTCTTTTCAC
1 CTTGGATCTCTTTTCAC
321854 AAGGAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.29, G:0.12, T:0.47
Consensus pattern (17 bp):
CTTGGATCTCTTTTCAC
Found at i:326949 original size:16 final size:16
Alignment explanation
Indices: 326914--326949 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
326904 TTTATCAATT
*
326914 TAATTTTAATTTAATA
1 TAATTTTAAATTAATA
326930 -AATTTTAAATTAATA
1 TAATTTTAAATTAATA
326945 TAATT
1 TAATT
326950 ACACATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTTTAAATTAATA
Found at i:328315 original size:23 final size:22
Alignment explanation
Indices: 328278--328320 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
328268 ACAATTTTTT
*
328278 TTAAAAAAATTAAAATTAAATA
1 TTAAAAAAATTAAAACTAAATA
*
328300 TTAAAATAGATTAAAACTAAA
1 TTAAAA-AAATTAAAACTAAA
328321 AATTTAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TTAAAAAAATTAAAACTAAATA
Found at i:332238 original size:264 final size:264
Alignment explanation
Indices: 331768--332296 Score: 1031
Period size: 264 Copynumber: 2.0 Consensus size: 264
331758 GGTCTCATTC
331768 ATTCTCTATAGGAGTGACGGAAGTTCTTAGCACAAACCTCCTAATAGAACTAAGGGCTGATGACA
1 ATTCTCTATAGGAGTGACGGAAGTTCTTAGCACAAACCTCCTAATAGAACTAAGGGCTGATGACA
331833 TAGATTTCGTTTTTCAAAGGTAAGTAACGCTGCTACAATTGATAACTATCACATATTACAATATA
66 TAGATTTCGTTTTTCAAAGGTAAGTAACGCTGCTACAATTGATAACTATCACATATTACAATATA
331898 GACGACTTGAACTCATTCTTATTATTTTCAGCAAATGACTCATCAAGAGCATGGATTTGCAATAT
131 GACGACTTGAACTCATTCTTATTATTTTCAGCAAATGACTCATCAAGAGCATGGATTTGCAATAT
331963 TAAACTTGATTATATCAAGTCTTTGTTTACTTATCATCTAGGAAAAAGTACCGAGGATTATGCTC
196 TAAACTTGATTATATCAAGTCTTTGTTTACTTATCATCTAGGAAAAAGTACCGAGGATTATGCTC
332028 TTTG
261 TTTG
332032 ATTCTCTATAGGAGTGACGGAAGTTCTTAGCACAAACCTCCTAATAGAACTAAGGGCTGATGACA
1 ATTCTCTATAGGAGTGACGGAAGTTCTTAGCACAAACCTCCTAATAGAACTAAGGGCTGATGACA
332097 TAGATTTCGTTTTTCAAAGGTAAGTAACGCTGCTACAATTGATAACTATCACATATTACAATATA
66 TAGATTTCGTTTTTCAAAGGTAAGTAACGCTGCTACAATTGATAACTATCACATATTACAATATA
*
332162 GATGACTTGAACTCATTCTTATTATTTTCAGCAAATGACTCATCAAGAGCATGGATTTGCAATAT
131 GACGACTTGAACTCATTCTTATTATTTTCAGCAAATGACTCATCAAGAGCATGGATTTGCAATAT
* *
332227 TCAACTTGATTATATCAAGTTTTTGTTTACTTATCATCTAGGAAAAAGTACCGAGGATTATGCTC
196 TAAACTTGATTATATCAAGTCTTTGTTTACTTATCATCTAGGAAAAAGTACCGAGGATTATGCTC
332292 TTTG
261 TTTG
332296 A
1 A
332297 GAAGGACTCG
Statistics
Matches: 262, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
264 262 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (264 bp):
ATTCTCTATAGGAGTGACGGAAGTTCTTAGCACAAACCTCCTAATAGAACTAAGGGCTGATGACA
TAGATTTCGTTTTTCAAAGGTAAGTAACGCTGCTACAATTGATAACTATCACATATTACAATATA
GACGACTTGAACTCATTCTTATTATTTTCAGCAAATGACTCATCAAGAGCATGGATTTGCAATAT
TAAACTTGATTATATCAAGTCTTTGTTTACTTATCATCTAGGAAAAAGTACCGAGGATTATGCTC
TTTG
Found at i:345145 original size:14 final size:14
Alignment explanation
Indices: 345126--345192 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 14
345116 GAAGCCTGAG
*
345126 GAGCCGTTTGAGTC
1 GAGCCGTTTGAGCC
*
345140 GAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTGAGC-----C
345159 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
*
345173 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
345187 GAGCCG
1 GAGCCG
345193 AGCCGTTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 31 0.70
19 13 0.30
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.21
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:345161 original size:19 final size:19
Alignment explanation
Indices: 345134--345216 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
345124 AGGAGCCGTT
* *
345134 TGAGTCGAGCCGCTTGAGC
1 TGAGCCGAGCCGTTTGAGC
345153 TGAGCCGAGCCG-TT----
1 TGAGCCGAGCCGTTTGAGC
345167 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
345186 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
*
345205 TGAGCCAAGCCG
1 TGAGCCGAGCCG
345217 AGCCGCCTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.21
15 2 0.04
18 2 0.04
19 41 0.72
ACGTcount: A:0.17, C:0.28, G:0.36, T:0.19
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:345163 original size:33 final size:33
Alignment explanation
Indices: 345126--345210 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
345116 GAAGCCTGAG
*
345126 GAGCCGTTTGAGTCGAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
345159 GAGCCGTTTGAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
345192 GAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCC
345211 AAGCCGAGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.21
Consensus pattern (33 bp):
GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
Found at i:345210 original size:14 final size:14
Alignment explanation
Indices: 345153--345192 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
345143 CCGCTTGAGC
345153 TGAGCCGAGCCGTT
1 TGAGCCGAGCCGTT
345167 TGAGCCGAGCCGTT
1 TGAGCCGAGCCGTT
*
345181 TGAGCTGAGCCG
1 TGAGCCGAGCCG
345193 AGCCGTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (14 bp):
TGAGCCGAGCCGTT
Found at i:346391 original size:18 final size:18
Alignment explanation
Indices: 346365--346399 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
346355 TCGAAAGGAC
*
346365 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
346383 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
346400 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:350132 original size:14 final size:14
Alignment explanation
Indices: 350113--350179 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 14
350103 GAAGCCTGAG
*
350113 GAGCCGTTTGAGTC
1 GAGCCGTTTGAGCC
*
350127 GAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTGAGC-----C
350146 GAGCCGTTTGAGCC
1 GAGCCGTTTGAGCC
*
350160 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCC
350174 GAGCCG
1 GAGCCG
350180 AGCCGTTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 31 0.70
19 13 0.30
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.21
Consensus pattern (14 bp):
GAGCCGTTTGAGCC
Found at i:350148 original size:19 final size:19
Alignment explanation
Indices: 350121--350203 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
350111 AGGAGCCGTT
* *
350121 TGAGTCGAGCCGCTTGAGC
1 TGAGCCGAGCCGTTTGAGC
350140 TGAGCCGAGCCG-TT----
1 TGAGCCGAGCCGTTTGAGC
350154 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
350173 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
*
350192 TGAGCCAAGCCG
1 TGAGCCGAGCCG
350204 AGCCGCCTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.21
15 2 0.04
18 2 0.04
19 41 0.72
ACGTcount: A:0.17, C:0.28, G:0.36, T:0.19
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:350150 original size:33 final size:33
Alignment explanation
Indices: 350113--350197 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
350103 GAAGCCTGAG
*
350113 GAGCCGTTTGAGTCGAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
350146 GAGCCGTTTGAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
350179 GAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCC
350198 AAGCCGAGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.21
Consensus pattern (33 bp):
GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
Found at i:350197 original size:14 final size:14
Alignment explanation
Indices: 350140--350179 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
350130 CCGCTTGAGC
350140 TGAGCCGAGCCGTT
1 TGAGCCGAGCCGTT
350154 TGAGCCGAGCCGTT
1 TGAGCCGAGCCGTT
*
350168 TGAGCTGAGCCG
1 TGAGCCGAGCCG
350180 AGCCGTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (14 bp):
TGAGCCGAGCCGTT
Found at i:354934 original size:19 final size:19
Alignment explanation
Indices: 354907--354988 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
354897 AGGAGCCGTT
* *
354907 TGAGTCGAGCCGCTTGAGC
1 TGAGCCGAGCCGTTTGAGC
354926 TGAGCCGAGCCG--T----
1 TGAGCCGAGCCGTTTGAGC
354939 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
354958 TGAGCCGAGCCGTTTGAGC
1 TGAGCCGAGCCGTTTGAGC
*
354977 TGAGCCAAGCCG
1 TGAGCCGAGCCG
354989 AGCCGCCTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 12 0.22
15 1 0.02
17 1 0.02
19 41 0.75
ACGTcount: A:0.17, C:0.28, G:0.37, T:0.18
Consensus pattern (19 bp):
TGAGCCGAGCCGTTTGAGC
Found at i:354944 original size:13 final size:14
Alignment explanation
Indices: 354926--354964 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
354916 CCGCTTGAGC
354926 TGAGCCGAGCCG-T
1 TGAGCCGAGCCGTT
354939 TGAGCCGAGCCGTT
1 TGAGCCGAGCCGTT
*
354953 TGAGCTGAGCCG
1 TGAGCCGAGCCG
354965 AGCCGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.18
Consensus pattern (14 bp):
TGAGCCGAGCCGTT
Found at i:354948 original size:32 final size:33
Alignment explanation
Indices: 354899--354982 Score: 134
Period size: 32 Copynumber: 2.6 Consensus size: 33
354889 GAAGCCTGAG
*
354899 GAGCCGTTTGAGTCGAGCCGCTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
354932 GAGCCG-TTGAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
*
354964 GAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCCGAGCC
354983 AAGCCGAGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 30 0.64
33 17 0.36
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.20
Consensus pattern (33 bp):
GAGCCGTTTGAGCCGAGCCGCTTGAGCTGAGCC
Found at i:354982 original size:14 final size:14
Alignment explanation
Indices: 354899--354964 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
354889 GAAGCCTGAG
354899 GAGCCGTTTGAG-T
1 GAGCCGTTTGAGCT
*
354912 CGAGCCGCTTGAGCT
1 -GAGCCGTTTGAGCT
* *
354927 GAGCCGAGCCGTTGAGCC
1 GAGCC--G--TTTGAGCT
354945 GAGCCGTTTGAGCT
1 GAGCCGTTTGAGCT
354959 GAGCCG
1 GAGCCG
354965 AGCCGTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
14 28 0.67
15 1 0.02
16 2 0.05
18 11 0.26
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.20
Consensus pattern (14 bp):
GAGCCGTTTGAGCT
Found at i:355198 original size:33 final size:34
Alignment explanation
Indices: 355133--355198 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
355123 CGACGTTCCA
* *
355133 AATCCGATTCCGTAATCCGTTTTCCAAAATTCGG
1 AATCCGAATCCGTAATCCGGTTTCCAAAATTCGG
*
355167 AATCCGAATCCG-AAT-CGGTTTCGCTAAATTCG
1 AATCCGAATCCGTAATCCGGTTTC-CAAAATTCG
355199 ACCCGGTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 6 0.21
33 11 0.39
34 11 0.39
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (34 bp):
AATCCGAATCCGTAATCCGGTTTCCAAAATTCGG
Found at i:360546 original size:22 final size:24
Alignment explanation
Indices: 360503--360546 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
360493 CAACAAAAAT
* *
360503 TTCATATTTTTTAATTATAAAAGA
1 TTCATATTTTTTAATAAAAAAAGA
360527 TTCAT-TTTTTT-ATAAAAAAA
1 TTCATATTTTTTAATAAAAAAA
360547 AATATGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 6 0.33
24 5 0.28
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (24 bp):
TTCATATTTTTTAATAAAAAAAGA
Found at i:364861 original size:22 final size:22
Alignment explanation
Indices: 364836--364896 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
364826 ACGATAGTGA
364836 AACTTGTTGGTCAAGGTGTACT
1 AACTTGTTGGTCAAGGTGTACT
364858 AACTTGTTGGTCAAGGTGTACT
1 AACTTGTTGGTCAAGGTGTACT
364880 AACTTGTTGGTCAAGGT
1 AACTTGTTGGTCAAGGT
364897 TGAGTATCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (22 bp):
AACTTGTTGGTCAAGGTGTACT
Found at i:366386 original size:11 final size:11
Alignment explanation
Indices: 366362--366405 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
366352 TTGGTGCTGG
366362 AAACAAGATAA
1 AAACAAGATAA
* *
366373 AAATAAGATTA
1 AAACAAGATAA
366384 AAACAAGATAA
1 AAACAAGATAA
*
366395 AGA-AAGATAA
1 AAACAAGATAA
366405 A
1 A
366406 TGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:381608 original size:22 final size:23
Alignment explanation
Indices: 381583--381627 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
381573 TTGCTCGGTA
381583 CGGAAT-T-ACTAATCAAAGGACT
1 CGGAATATCACTAA-CAAAGGACT
381605 CGGAATATGCACTAACAAAGGAC
1 CGGAATAT-CACTAACAAAGGAC
381628 CTACATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 8 0.40
25 5 0.25
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (23 bp):
CGGAATATCACTAACAAAGGACT
Found at i:386896 original size:15 final size:15
Alignment explanation
Indices: 386876--386905 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
386866 TTCTCAACCA
386876 CATCCTTTGGAAGAG
1 CATCCTTTGGAAGAG
386891 CATCCTTTGGAAGAG
1 CATCCTTTGGAAGAG
386906 TTAATTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (15 bp):
CATCCTTTGGAAGAG
Found at i:390453 original size:20 final size:21
Alignment explanation
Indices: 390398--390442 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
390388 ATGATTTTGA
* *
390398 AAAATTAAAAGTTTAAGTACT
1 AAAATTGATAGTTTAAGTACT
*
390419 AAAATTGATAGTTTAGGTACT
1 AAAATTGATAGTTTAAGTACT
390440 AAA
1 AAA
390443 TATATAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (21 bp):
AAAATTGATAGTTTAAGTACT
Found at i:391083 original size:23 final size:23
Alignment explanation
Indices: 391051--391096 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
391041 ATTGATTGTG
*
391051 ATAATAATTTCAAACTAATAATA
1 ATAATAATTTCAAAATAATAATA
* *
391074 ATAATGATTTTAAAATAATAATA
1 ATAATAATTTCAAAATAATAATA
391097 TGTTAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
ATAATAATTTCAAAATAATAATA
Found at i:391104 original size:16 final size:17
Alignment explanation
Indices: 391070--391104 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
391060 TCAAACTAAT
*
391070 AATAATAATGATTTTAA
1 AATAATAATGATGTTAA
391087 AATAATAAT-ATGTTAA
1 AATAATAATGATGTTAA
391103 AA
1 AA
391105 ACCAAACCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
AATAATAATGATGTTAA
Found at i:391957 original size:14 final size:15
Alignment explanation
Indices: 391938--391968 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
391928 TGCACAGAAG
391938 AAAGAG-AGAAAAGA
1 AAAGAGAAGAAAAGA
391952 AAAGAGAAGAAAAGA
1 AAAGAGAAGAAAAGA
391967 AA
1 AA
391969 CCATGGGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGAAAAGA
Found at i:391959 original size:12 final size:13
Alignment explanation
Indices: 391935--391968 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
391925 ACGTGCACAG
391935 AAGAAAGAGAGAA
1 AAGAAAGAGAGAA
391948 AAGAAAAGAGAAGAA
1 AAG-AAAGAG-AGAA
391963 AAGAAA
1 AAGAAA
391969 CCATGGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.16
14 9 0.47
15 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGAAAGAGAGAA
Found at i:393787 original size:20 final size:20
Alignment explanation
Indices: 393762--393807 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
393752 TCAAATGAAA
* *
393762 AAAAATCAAGATTTTAGATT
1 AAAAATCAAGATTTTACACT
* *
393782 AAAAATCGAGGTTTTACACT
1 AAAAATCAAGATTTTACACT
393802 AAAAAT
1 AAAAAT
393808 TTTCTTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (20 bp):
AAAAATCAAGATTTTACACT
Found at i:394281 original size:2 final size:2
Alignment explanation
Indices: 394274--394303 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
394264 ATAACGATCT
394274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394304 CCATGTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413518 original size:217 final size:213
Alignment explanation
Indices: 413081--414447 Score: 1076
Period size: 217 Copynumber: 6.4 Consensus size: 213
413071 AACTTGAACG
*
413081 AAGACCTCCACACGTGTTACCCCTTTATCGAGGATGGTTTAGGGTTTAAC-AGGTATCGAGGTTA
1 AAGACCTCCACACGTGTTACCCCTTGATCGAGGATGGTTTAGGGTTTAACGA-GTATCGAGGTTA
* * * * * *
413145 CAATAATCTCTTTTCACTTCATTTATCATTGAAGTGACAAAG-AATTGTAACTTGAGCGCACCCA
65 CAATAATCTCTTTTCACTTCTTTTTTCACTAAAATAACAAAGAAATTGTAACTTGAGCGCA-CCA
* * * * * * *
413209 ACCCAAACCTTCAACTCCTCCATCGAGATAGCACTCATAAGGCATTGGTGTTTCTTTTCTTAAAG
129 A-CCAGACCTTCAACTCCTCCATCGAGACAACACTCGTAGGGCA-TGATGTTTCTTTTCTTAAAA
* *
413274 CACACGAGGGAAACACCACG-AA
192 CACACAAGGAAAACACCA-GAAA
* * * * *
413296 AAGACCTTCACACTTGTTACCCCTTGATCGAGGAAGGTTTAGGGTTTTACGAGTGTCGAGGTTAC
1 AAGACCTCCACACGTGTTACCCCTTGATCGAGGATGGTTTAGGGTTTAACGAGTATCGAGGTTAC
* * * * * *
413361 AATAGTCTCTTCTCACTTCTTCTTTTCACTGAAATAACAAAGAAGTTGTAACTTGAGTGCACTTA
66 AATAATCTCTTTTCACTTCTT-TTTTCACTAAAATAACAAAGAAATTGTAACTTGAGCGCAC-CA
* ** *
413426 ACCTAGACCTTCAAGTCCTCCATAAAGACAACACTTGTAGGGCATCGATGTTTCTTTTCTTAAAA
129 ACC-AGACCTTCAACTCCTCCATCGAGACAACACTCGTAGGGCAT-GATGTTTCTTTTCTTAAAA
* *
413491 CACACAAGGAAAAGACCTGAAA
192 CACACAAGGAAAACACCAGAAA
* * * *
413513 AAGACCTCCATATGTGTTACCCTTTTAAAT-GAGGATGGTTTAGGGTTTAACG-GATATCGAGGT
1 AAGACCTCCACACGTGTTACCC-CTT-GATCGAGGATGGTTTAGGGTTTAACGAG-TATCGAGGT
* *
413576 TACAACAATCTCTTTTCACTTTCTTTTTTCA-TAAAAATAACAAAGAAGTTGT-A----A--G--
63 TACAATAATCTCTTTTCAC-TTCTTTTTTCACT-AAAATAACAAAGAAATTGTAACTTGAGCGCA
* * * *
413631 -C--CCGGACCTTCAACTCCTCTATCGAGACAACACTCGTAGTGCATTGGTAT-TTTTTTTTCTT
126 CCAACCAGACCTTCAACTCCTCCATCGAGACAACACTCGTAGGGCA-T-G-ATGTTTCTTTTCTT
* *
413692 AAAACACACAAGGAAAAGACTA-AGAA
188 AAAACACACAAGGAAAACACCAGA-AA
* ** * * * * *
413718 AAGACATCCACACGTGTTATTCCTTGACCGAGGATAGTTTAAGGTTTAA-TAGGTATTGAGGTTA
1 AAGACCTCCACACGTGTTACCCCTTGATCGAGGATGGTTTAGGGTTTAACGA-GTATCGAGGTTA
* * * * **
413782 CAACAACCTCTTTTCACTTCTCTTTCTCACTAAAATAACAAAGAAATTATAACTTGAATGCACCA
65 CAATAATCTCTTTTCACTTCT-TTTTTCACTAAAATAACAAAGAAATTGTAACTTGAGCGCACCA
* * *
413847 ACTC-GAACCTTCAACTCCTCCATCGAGACAACACTCGTAAGACATTAGTGTTTCTTTTCTTAAA
129 AC-CAG-ACCTTCAACTCCTCCATCGAGACAACACTCGTAGGGCATGA-TGTTTCTTTTCTTAAA
** **
413911 ACACACGAACTAAAACACCAGGTA
191 ACACAC-AAGGAAAACACCAGAAA
* * * * * * * *
413935 AATACTTCTATACGTGTTA-CCCTTGA-CTAGGATGGTTTAGGTTTTATCGGGTATCGAGGTTAC
1 AAGACCTCCACACGTGTTACCCCTTGATCGAGGATGGTTTAGGGTTTAACGAGTATCGAGGTTAC
** * *
413998 AATGGT-TTTTTTCACTTCTTTTTTTAAACTAAAATAACAAAGAAATTGTAACTTGAGCGCACTC
66 AATAATCTCTTTTCACTTC-TTTTTT-CACTAAAATAACAAAGAAATTGTAACTTGAGCGCAC-C
* * ** * * *
414062 AACCCGAACCTTGAACTTTTCCATCGA-ACATCACTCGTAGGGCATTAGTGTTTCTTTTTTTAAA
128 AACCAG-ACCTTCAACTCCTCCATCGAGACAACACTCGTAGGGCATGA-TGTTTCTTTTCTTAAA
**
414126 A-AGCATGAGGAAAACACCAAGAAA
191 ACA-CACAAGGAAAACACC-AGAAA
* * * * * * * *
414150 AA-ACCTCCACATGCGTTACCCTTTG-CCTGAGGATGATTTAGGGTTTAACAAGCATCGAGATTA
1 AAGACCTCCACACGTGTTACCCCTTGATC-GAGGATGGTTTAGGGTTTAACGAGTATCGAGGTTA
* * * * *
414213 C-ATCAGTCTCTTCTCACTTCGTTTTTTCATTAAAATAACAAAGAAATTGTAACTCGAACGCACC
65 CAAT-AATCTCTTTTCACTTC-TTTTTTCACTAAAATAACAAAGAAATTGTAACTTGAGCGCA-C
* * * * ** *
414277 CGACCCGAACCTTCAACTCCT-CATTCGATATAACACTCGTAGGAAATTGGTGTTTCTTTTCTTA
127 CAACCAG-ACCTTCAACTCCTCCA-TCGAGACAACACTCGTAGGGCA-TGATGTTTCTTTTCTTA
* * *
414341 AAACACACGA-GAAAAGTACCAGGAA
189 AAACACACAAGGAAAA-CACCAGAAA
* * * * *
414366 AAGACCTCTACACGTATTA-CCCTTGATCGAGGATGATTTAAGGTTTAAC-ATGTATCGAGGATA
1 AAGACCTCCACACGTGTTACCCCTTGATCGAGGATGGTTTAGGGTTTAACGA-GTATCGAGGTTA
*
414429 C-ATCAATCTATTTTCACTT
65 CAAT-AATCTCTTTTCACTT
414448 ATAAATCTAA
Statistics
Matches: 924, Mismatches: 169, Indels: 117
0.76 0.14 0.10
Matches are distributed among these distances:
203 5 0.01
204 103 0.11
205 56 0.06
206 2 0.00
209 1 0.00
211 2 0.00
213 1 0.00
214 38 0.04
215 192 0.21
216 216 0.23
217 229 0.25
218 72 0.08
219 7 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (213 bp):
AAGACCTCCACACGTGTTACCCCTTGATCGAGGATGGTTTAGGGTTTAACGAGTATCGAGGTTAC
AATAATCTCTTTTCACTTCTTTTTTCACTAAAATAACAAAGAAATTGTAACTTGAGCGCACCAAC
CAGACCTTCAACTCCTCCATCGAGACAACACTCGTAGGGCATGATGTTTCTTTTCTTAAAACACA
CAAGGAAAACACCAGAAA
Found at i:413795 original size:204 final size:203
Alignment explanation
Indices: 413431--413826 Score: 480
Period size: 204 Copynumber: 1.9 Consensus size: 203
413421 ACTTAACCTA
* *
413431 GACCTTCAAGTCCTCCATAAAGACAACACTTGTAGGGCATCGATGTTTCTTTTCTTAAAACACAC
1 GACCTTCAACTCCTCCATAAAGACAACACTCGTAGGGCATCGATGTTTCTTTTCTTAAAACACAC
* * * * * * *
413496 AAGGAAAAGACCTGAAAAAGACCTCCATATGTGTTACCCTTTTAAATGAGGATGGTTTAGGGTTT
66 AAGGAAAAGACCTAAAAAAGACATCCACACGTGTTACCC-TTTAAACGAGGATAGTTTAAGGTTT
* * *
413561 AACGGATATCGAGGTTACAACAATCTCTTTTCACTT-TCTTTTTTCA-TAAAAATAACAAAGAAG
130 AAAGGATATCGAGGTTACAACAACCTCTTTTCACTTCTC-TTTCTCACT-AAAATAACAAAGAAG
413624 TTGTAAGCCCG
193 TTGTAAGCCCG
* ** * * *
413635 GACCTTCAACTCCTCTATCGAGACAACACTCGTAGTGCATTGGTAT-TTTTTTTTCTTAAAACAC
1 GACCTTCAACTCCTCCATAAAGACAACACTCGTAGGGCA-TCG-ATGTTTCTTTTCTTAAAACAC
* * *
413699 ACAAGGAAAAGA-CTAAGAAAAGACATCCACACGTGTTATTCC-TTGACCGAGGATAGTTTAAGG
64 ACAAGGAAAAGACCTAA-AAAAGACATCCACACGTGTTA-CCCTTTAAACGAGGATAGTTTAAGG
*
413762 TTTAATAGG-TATTGAGGTTACAACAACCTCTTTTCACTTCTCTTTCTCACTAAAATAACAAAGA
127 TTTAA-AGGATATCGAGGTTACAACAACCTCTTTTCACTTCTCTTTCTCACTAAAATAACAAAGA
413826 A
191 A
413827 ATTATAACTT
Statistics
Matches: 163, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
204 105 0.64
205 54 0.33
206 4 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (203 bp):
GACCTTCAACTCCTCCATAAAGACAACACTCGTAGGGCATCGATGTTTCTTTTCTTAAAACACAC
AAGGAAAAGACCTAAAAAAGACATCCACACGTGTTACCCTTTAAACGAGGATAGTTTAAGGTTTA
AAGGATATCGAGGTTACAACAACCTCTTTTCACTTCTCTTTCTCACTAAAATAACAAAGAAGTTG
TAAGCCCG
Found at i:414099 original size:215 final size:213
Alignment explanation
Indices: 413631--414447 Score: 693
Period size: 216 Copynumber: 3.8 Consensus size: 213
413621 AAGTTGTAAG
* * * * *
413631 CCCGGACCTTCAACTCCTCTATCGAGACAACACTCGTAGTG-CATTGGTATTTTTTTTTCTTAAA
1 CCCGAACCTTCAACTCCTCCATCGAGACAACACTCGTAG-GACATTAGT-GTTTCTTTTCTTAAA
* * * * * * * *
413695 ACACAC-AAGGAAAAGACTAAGAAAAGACATCCACACGTGTTATTCCTTGACCGAGGAT-AGTTT
64 ACACACGAA--AAAACACCAGGAAAAAACCTCTACACGTGTTA-CCCTTGA-CTAGGATGA-TTT
* * * * * * ** * *
413758 AAGG-TTTAATAGGTATTGAGGTTACAACAACCTCTTTTCACTTCTCTTTCTCACTAAAATAACA
124 -AGGTTTTAACAAGCATCGAGATTACATCAGTCTCTTTTCACTTCTTTTTTTCACTAAAATAACA
* *
413822 AAGAAATTATAACTTGAATGCACCAA
188 AAGAAATTGTAACTTGAACGCACCAA
* *
413848 CTCGAACCTTCAACTCCTCCATCGAGACAACACTCGTAAGACATTAGTGTTTCTTTTCTTAAAAC
1 CCCGAACCTTCAACTCCTCCATCGAGACAACACTCGTAGGACATTAGTGTTTCTTTTCTTAAAAC
* * * * *
413913 ACACGAACTAAAACACCAGGTAAATACTTCTATACGTGTTACCCTTGACTAGGATGGTTTAGGTT
66 ACACGAA--AAAACACCAGGAAAAAACCTCTACACGTGTTACCCTTGACTAGGATGATTTAGGTT
* ** * * * * *
413978 TTATCGGGTATCGAGGTTACAAT-GGT-TTTTTTCACTTCTTTTTTTAAACTAAAATAACAAAGA
129 TTAACAAGCATCGAGATTAC-ATCAGTCTCTTTTCACTTCTTTTTTT-CACTAAAATAACAAAGA
*
414041 AATTGTAACTTGAGCGCACTCAA
192 AATTGTAACTTGAACGCAC-CAA
* ** * * *
414064 CCCGAACCTTGAACTTTTCCATCGA-ACATCACTCGTAGGGCATTAGTGTTTCTTTTTTTAAAA-
1 CCCGAACCTTCAACTCCTCCATCGAGACAACACTCGTAGGACATTAGTGTTTCTTTTCTTAAAAC
* * * * * * *
414127 AGCATGAGGAAAACACCAAGAAAAAACCTCCACATGCGTTACCCTTTGCCTGAGGATGATTTAGG
66 A-CACGA-AAAAACACCAGGAAAAAACCTCTACACGTGTTACCC-TTGACT-AGGATGATTTAGG
* * * *
414192 GTTTAACAAGCATCGAGATTACATCAGTCTCTTCTCACTTCGTTTTTTCATTAAAATAACAAAGA
127 TTTTAACAAGCATCGAGATTACATCAGTCTCTTTTCACTTCTTTTTTTCACTAAAATAACAAAGA
* *
414257 AATTGTAACTCGAACGCACCCGA
192 AATTGTAACTTGAACGCA-CCAA
* * * *
414280 CCCGAACCTTCAACTCCT-CATTCGATATAACACTCGTAGGAAATTGGTGTTTCTTTTCTTAAAA
1 CCCGAACCTTCAACTCCTCCA-TCGAGACAACACTCGTAGGACATTAGTGTTTCTTTTCTTAAAA
** * * *
414344 CACACGAGAAAAGTACCAGGAAAAGACCTCTACACGTATTACCCTTGATCGAGGATGATTTAAGG
65 CACACGA-AAAAACACCAGGAAAAAACCTCTACACGTGTTACCCTTGA-CTAGGATGATTT-AGG
* * * *
414409 -TTTAACATGTATCGAGGA-TACATCAATCTATTTTCACTT
127 TTTTAACAAGCATCGA-GATTACATCAGTCTCTTTTCACTT
414448 ATAAATCTAA
Statistics
Matches: 484, Mismatches: 96, Indels: 41
0.78 0.15 0.07
Matches are distributed among these distances:
214 47 0.10
215 105 0.22
216 177 0.37
217 154 0.32
218 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (213 bp):
CCCGAACCTTCAACTCCTCCATCGAGACAACACTCGTAGGACATTAGTGTTTCTTTTCTTAAAAC
ACACGAAAAAACACCAGGAAAAAACCTCTACACGTGTTACCCTTGACTAGGATGATTTAGGTTTT
AACAAGCATCGAGATTACATCAGTCTCTTTTCACTTCTTTTTTTCACTAAAATAACAAAGAAATT
GTAACTTGAACGCACCAA
Found at i:419014 original size:16 final size:18
Alignment explanation
Indices: 418993--419029 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
418983 TTAAAAATCA
*
418993 TTTTAATTTTA-ATTT-T
1 TTTTAAATTTATATTTAT
419009 TTTTAAATTTATATTTAT
1 TTTTAAATTTATATTTAT
419027 TTT
1 TTT
419030 GACCTGACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTAAATTTATATTTAT
Found at i:421621 original size:257 final size:257
Alignment explanation
Indices: 421128--421641 Score: 1012
Period size: 257 Copynumber: 2.0 Consensus size: 257
421118 TTCCCCAATT
421128 TTTATGTTGCCATTGTGACATAATTTGCTCTGTGCTAAAAAGGATTCTGCTTTTGGGTTGAAGTT
1 TTTATGTTGCCATTGTGACATAATTTGCTCTGTGCTAAAAAGGATTCTGCTTTTGGGTTGAAGTT
421193 CTTAATTGATTATAATATATGTCTCTTCACTTCCTTTGTTGAGTACAGCATGAGGACTGCATTAA
66 CTTAATTGATTATAATATATGTCTCTTCACTTCCTTTGTTGAGTACAGCATGAGGACTGCATTAA
421258 AGATTGTGACAAGGCCGTTGAAAGAGGTAGAGAGCTCCGAGCAGACTATAAAATGATAGCAAGAG
131 AGATTGTGACAAGGCCGTTGAAAGAGGTAGAGAGCTCCGAGCAGACTATAAAATGATAGCAAGAG
421323 CTTTTGACGAGGAAGGGGACTGCTTTGGTGAAGATGCGAAATGCTCGAAAGATTATGAACCG
196 CTTTTGACGAGGAAGGGGACTGCTTTGGTGAAGATGCGAAATGCTCGAAAGATTATGAACCG
421385 TTTATGTTGCCATTGTGACATAATTTGCTCTGTGCTAAAAAGGATTCTGCTTTTGGGTTGAAGTT
1 TTTATGTTGCCATTGTGACATAATTTGCTCTGTGCTAAAAAGGATTCTGCTTTTGGGTTGAAGTT
421450 CTTAATTGATTATAATATATGTCTCTTCACTTCCTTTGTTGAGTACAGCATGAGGACTGCATTAA
66 CTTAATTGATTATAATATATGTCTCTTCACTTCCTTTGTTGAGTACAGCATGAGGACTGCATTAA
421515 AGATTGTGACAAGGCCGTTGAAAGAGGTAGAGAGCTCCGAGCAGACTATAAAATGATAGCAAGAG
131 AGATTGTGACAAGGCCGTTGAAAGAGGTAGAGAGCTCCGAGCAGACTATAAAATGATAGCAAGAG
421580 C-TTTGACGAGGAAGGGGACTGCTTTGGTGAAGATGGCGAAATGCTCGAAAGATTATGAACCG
196 CTTTTGACGAGGAAGGGGACTGCTTTGGTGAAGAT-GCGAAATGCTCGAAAGATTATGAACCG
421642 GCGACAGAGA
Statistics
Matches: 256, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
256 33 0.13
257 223 0.87
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (257 bp):
TTTATGTTGCCATTGTGACATAATTTGCTCTGTGCTAAAAAGGATTCTGCTTTTGGGTTGAAGTT
CTTAATTGATTATAATATATGTCTCTTCACTTCCTTTGTTGAGTACAGCATGAGGACTGCATTAA
AGATTGTGACAAGGCCGTTGAAAGAGGTAGAGAGCTCCGAGCAGACTATAAAATGATAGCAAGAG
CTTTTGACGAGGAAGGGGACTGCTTTGGTGAAGATGCGAAATGCTCGAAAGATTATGAACCG
Found at i:427295 original size:21 final size:20
Alignment explanation
Indices: 427269--427312 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
427259 TGATTTCTGG
* *
427269 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
427290 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
427310 CAA
1 CAA
427313 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:428328 original size:31 final size:30
Alignment explanation
Indices: 428290--428399 Score: 184
Period size: 31 Copynumber: 3.6 Consensus size: 30
428280 GGGTCGAGGG
428290 TTTACCTATGTTCTTCGGGACATATGGACT
1 TTTACCTATGTTCTTCGGGACATATGGACT
428320 ATTTACCTATGTTCTTCGGGACATATGGACT
1 -TTTACCTATGTTCTTCGGGACATATGGACT
428351 GTTTACCTATGTTCTTCGGGACATATGGACT
1 -TTTACCTATGTTCTTCGGGACATATGGACT
* *
428382 GTTACCTAGGTTCTTCGG
1 TTTACCTATGTTCTTCGG
428400 AATCTATGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 16 0.21
31 60 0.79
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (30 bp):
TTTACCTATGTTCTTCGGGACATATGGACT
Found at i:428360 original size:62 final size:61
Alignment explanation
Indices: 428289--428412 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 61
428279 AGGGTCGAGG
* * *
428289 GTTTACCTATGTTCTTCGGGACATATGGACTATTTACCTATGTTCTTCGGGA-CATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT-GTTACCTAGGTTCTTCGGAATC-TATGGACT
428351 GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTAGGTTCTTCGGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTAGGTTCTTCGGAATCTATGGACT
428412 G
1 G
428413 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
61 26 0.45
62 32 0.55
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (61 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTAGGTTCTTCGGAATCTATGGACT
Found at i:432319 original size:47 final size:49
Alignment explanation
Indices: 432234--432327 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 49
432224 GACCATGTTC
432234 TAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTTGCT
1 TAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTTGCT
432283 TAAATTGACAAAGCTC-TT-TGGTTTAAAACAAGCTCCTAGAGCTTG
1 TAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTTG
432328 GTATGAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 27 0.60
48 2 0.04
49 16 0.36
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAATTGACAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTTGCT
Found at i:433394 original size:21 final size:23
Alignment explanation
Indices: 433361--433419 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
433351 TTGGTGCAGA
*
433361 GAGAATCGA-TCCCCCTATG-AG
1 GAGAACCGATTCCCCCTATGAAG
*
433382 G-GAACCGATTCCCCCTTTGAAG
1 GAGAACCGATTCCCCCTATGAAG
433404 GAGAACCGATTCCCCC
1 GAGAACCGATTCCCCC
433420 CCCCAAAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.18
21 10 0.30
22 3 0.09
23 14 0.42
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (23 bp):
GAGAACCGATTCCCCCTATGAAG
Found at i:435428 original size:24 final size:23
Alignment explanation
Indices: 435378--435451 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
435368 GTTTCAACTT
* *
435378 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
435401 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
435425 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
435448 TTTG
1 TTTG
435452 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:436309 original size:61 final size:61
Alignment explanation
Indices: 436234--436358 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
436224 CATAGGGGGT
436234 ATCGATTCCCTCACGCTCCAAGCTGTTTTATTAATTGTTTTCACACTAAAACGGCTATATG
1 ATCGATTCCCTCACGCTCCAAGCTGTTTTATTAATTGTTTTCACACTAAAACGGCTATATG
436295 ATCGATTCCCTCACGCTCCAAGCTGTTTTATTAATTGTTTTCACACTAAAACGGCTATATG
1 ATCGATTCCCTCACGCTCCAAGCTGTTTTATTAATTGTTTTCACACTAAAACGGCTATATG
436356 ATC
1 ATC
436359 TTCACTAATC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (61 bp):
ATCGATTCCCTCACGCTCCAAGCTGTTTTATTAATTGTTTTCACACTAAAACGGCTATATG
Found at i:437358 original size:7 final size:7
Alignment explanation
Indices: 437338--437393 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
437328 TATCACATAA
437338 TAGA-TT
1 TAGAGTT
437344 TAGAGTT
1 TAGAGTT
*
437351 TAGGGTT
1 TAGAGTT
437358 TA-AGTT
1 TAGAGTT
*
437364 TATAGTT
1 TAGAGTT
*
437371 TAGGGTT
1 TAGAGTT
*
437378 TAGGGTT
1 TAGAGTT
*
437385 TAGAATT
1 TAGAGTT
437392 TA
1 TA
437394 TTGTAAAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
6 9 0.21
7 33 0.79
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (7 bp):
TAGAGTT
Found at i:437370 original size:20 final size:20
Alignment explanation
Indices: 437342--437393 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
437332 ACATAATAGA
437342 TTTAGAGTTTAGGGTTTAAG
1 TTTAGAGTTTAGGGTTTAAG
* *
437362 TTTATAGTTTAGGGTTTAGGG
1 TTTAGAGTTTAGGGTTTA-AG
*
437383 TTTAGAATTTA
1 TTTAGAGTTTA
437394 TTGTAAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (20 bp):
TTTAGAGTTTAGGGTTTAAG
Found at i:437465 original size:14 final size:14
Alignment explanation
Indices: 437446--437492 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
437436 GTAAGTACAA
437446 TTTATGGTTTAAGG
1 TTTATGGTTTAAGG
*
437460 TTTATGATTT-AGG
1 TTTATGGTTTAAGG
437473 ATTTA-GAGTTTAAGG
1 -TTTATG-GTTTAAGG
437488 TTTAT
1 TTTAT
437493 TGCAATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.15
14 20 0.74
15 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (14 bp):
TTTATGGTTTAAGG
Found at i:449925 original size:10 final size:10
Alignment explanation
Indices: 449910--449936 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
449900 TCAATTGAAA
449910 GCTTTTGCAC
1 GCTTTTGCAC
449920 GCTTTTGCAC
1 GCTTTTGCAC
449930 GCTTTTG
1 GCTTTTG
449937 ATGAAACGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (10 bp):
GCTTTTGCAC
Found at i:452460 original size:25 final size:25
Alignment explanation
Indices: 452431--452481 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
452421 ATAAAGGTTA
452431 TTCTTTTTCCTATTCCAAGTAGTTT
1 TTCTTTTTCCTATTCCAAGTAGTTT
*
452456 TTCTTTTTCCTATTCCTAGTAGTTT
1 TTCTTTTTCCTATTCCAAGTAGTTT
452481 T
1 T
452482 GAAAATGGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.14, C:0.20, G:0.08, T:0.59
Consensus pattern (25 bp):
TTCTTTTTCCTATTCCAAGTAGTTT
Found at i:463341 original size:12 final size:12
Alignment explanation
Indices: 463321--463351 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
463311 TTACATATAC
*
463321 ATTTATAAAAAT
1 ATTTTTAAAAAT
463333 ATTTTTAAAAAT
1 ATTTTTAAAAAT
463345 ATTTTTA
1 ATTTTTA
463352 GATGATGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTTAAAAAT
Found at i:464815 original size:22 final size:21
Alignment explanation
Indices: 464781--464821 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
464771 ATAATTATTT
464781 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
464802 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
464822 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Done.