Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 6 of 208
Found at i:2039651 original size:23 final size:23
Alignment explanation
Indices: 2039620--2039665 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2039610 AAGTCAAAAG
*
2039620 ATTGATTCATAGATGCTATTAAC
1 ATTGATTCATAGATGCTAATAAC
* *
2039643 ATTGTTTCATAGATTCTAATAAC
1 ATTGATTCATAGATGCTAATAAC
2039666 TTAGCTTAGC
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:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (23 bp):
ATTGATTCATAGATGCTAATAAC
Found at i:2040751 original size:20 final size:21
Alignment explanation
Indices: 2040718--2040756 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2040708 GATTTGAATT
2040718 TTAAAATCTAAAAA-AAAAAA
1 TTAAAATCTAAAAATAAAAAA
* *
2040738 TTAAATTCTCAAAATAAAA
1 TTAAAATCTAAAAATAAAA
2040757 GTATAAGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (21 bp):
TTAAAATCTAAAAATAAAAAA
Found at i:2044191 original size:21 final size:21
Alignment explanation
Indices: 2044165--2044205 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2044155 ATCTGCTCAA
* *
2044165 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2044186 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2044206 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2050461 original size:20 final size:20
Alignment explanation
Indices: 2050416--2050463 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2050406 TACGTGTTTA
*
2050416 ATTATCATTTATAAATTAATT
1 ATTA-CATTTATAAATTAAGT
*
2050437 CTTACATTTGATAAA-TAAGT
1 ATTACATTT-ATAAATTAAGT
2050457 ATTACAT
1 ATTACAT
2050464 ATTTAAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
ATTACATTTATAAATTAAGT
Found at i:2050519 original size:15 final size:15
Alignment explanation
Indices: 2050482--2050520 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2050472 GGTGATAATT
* *
2050482 AATATTAATTTTTTA
1 AATATTAATATATTA
2050497 AA-ATTAATATATTA
1 AATATTAATATATTA
2050511 AATATTAATA
1 AATATTAATA
2050521 GATGAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATTAATATATTA
Found at i:2051639 original size:134 final size:133
Alignment explanation
Indices: 2051233--2051664 Score: 426
Period size: 133 Copynumber: 3.2 Consensus size: 133
2051223 TACTTTATGA
** * *
2051233 CTTTAGTGGCGC-TTCCACAAAAACGCCGCAAAAAATTGGAATATAGCGGTGTTTTCTGAGAAAC
1 CTTTAGTGGCGCATTGTA-AAAAACGCCGC-AAAAATTGGAATATAGCGGCGTTTT-AGAGAAAC
** * * * * *
2051297 GCTAGTAAAGATAACAAATTTGAA-GAAAAAATCTGAGCAAAACAATACCGTTTTATGGTTTCAT
63 GCCGGTAAAGATATCTAATTT-AAGGAAAAAATTTGAGCAAAACGATACCGTTTTATTGTTTCAT
*
2051361 TTTATTT
127 TTTATTG
* * * *
2051368 CTTTAGTGGCGCATTGTAAAAAACGCCGGAAAAGATT-GAAT-TGGCAGCGTTTTTAGAGAAACA
1 CTTTAGTGGCGCATTGTAAAAAACGCCGCAAAA-ATTGGAATATAGCGGCG-TTTTAGAGAAACG
* * * *
2051431 CCGGTAAAGATATCTAATTTGAGGAAAAAATTTG-GACAAAATGCTACCGTTTTATTGCTTCATT
64 CCGGTAAAGATATCTAATTTAAGGAAAAAATTTGAG-CAAAACGATACCGTTTTATTGTTTCATT
*
2051495 TTATTT
128 TTATTG
* * * *
2051501 CTTTAGTGGCGCATTGTAAAAAACGCCGCAAATATTGGGATATAGTGGCGTTATTGGAGAAACGC
1 CTTTAGTGGCGCATTGTAAAAAACGCCGCAAAAATTGGAATATAGCGGCGTT-TTAGAGAAACGC
* * * * * *
2051566 CGGTTAGGATATCTAATTTAAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTT
65 CGGTAAAGATATCTAATTTAAGGAAAAAATTTGAGCAAAACGATACCGTTTTATTGTTTCATTTT
2051631 -TATG
130 AT-TG
* *
2051635 CTTTAGTGGCGAAATGTTAAAAAAACGCCG
1 CTTTAGTGGCGCATTG-T-AAAAAACGCCG
2051665 GAAACGGTTC
Statistics
Matches: 246, Mismatches: 39, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
132 5 0.02
133 104 0.42
134 96 0.39
135 27 0.11
136 14 0.06
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (133 bp):
CTTTAGTGGCGCATTGTAAAAAACGCCGCAAAAATTGGAATATAGCGGCGTTTTAGAGAAACGCC
GGTAAAGATATCTAATTTAAGGAAAAAATTTGAGCAAAACGATACCGTTTTATTGTTTCATTTTA
TTG
Found at i:2052055 original size:21 final size:20
Alignment explanation
Indices: 2052016--2052068 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
2052006 TTTGTGTTCT
*
2052016 GGGCTTAGAGTTTAGGTTTA
1 GGGCTTAGAGTTGAGGTTTA
*
2052036 GGGCTTGGAGATTGAGGTTTA
1 GGGCTTAGAG-TTGAGGTTTA
* *
2052057 AGGTTTAGAGTT
1 GGGCTTAGAGTT
2052069 TACATTTCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.38
Consensus pattern (20 bp):
GGGCTTAGAGTTGAGGTTTA
Found at i:2057867 original size:522 final size:522
Alignment explanation
Indices: 2056882--2057927 Score: 1889
Period size: 522 Copynumber: 2.0 Consensus size: 522
2056872 AACATCTTAA
2056882 GGTTCGAATGTCCGATTCTTCGTATTTATACATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
1 GGTTCGAATGTCCGATTCTTCGTATTTATACATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
* *
2056947 CTTTCTTATTGGTTGGTGATACTGGAATTAAAAAAATGTATTCTCTGTGCTTAGGGTTTTCTGTG
66 CTTTCTTATTGGTTGGTGATACTAGAATTAAAAAAATGTATTCTCTGTGCTTAGGGTTTTCGGTG
*
2057012 TGTTCGACTGTTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTACTGTTTTT
131 TGTTCGACTATTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTACTGTTTTT
2057077 GTAAATGGTTTAATTTGTTAGGAACTGATTTTAAGTTTTGTTTTTTTTTTCTCCAGTTTTTGGTC
196 GTAAATGGTTTAATTTGTTAGGAACTGATTTTAAGTTTTG-TTTTTTTTTCTCCAGTTTTTGGTC
2057142 AATCCATTTCATTGCTTTCATTTCAGTTTTCTTCATCATTCTGAAGGTACAGAACACATGCTTTG
260 AATCCATTTCATTGCTTTCATTTCAGTTTTCTTCATCATTCTGAAGGTACAGAACACATGCTTTG
*
2057207 TTACTGTTTATTTGTTGAACTCATTTGGTACTGCTTTTAAAGTATGGAATTTTGATGTCTAGCTT
325 TTACTGTTTATTTGTTGAAATCATTTGGTACTGCTTTTAAAGTATGGAATTTTGATGTCTAGCTT
* * *
2057272 AGGGTTTAATTTATTAGTTTATAAAACTATTCTGTTAAATCTGGTGCAACCGATTACATTTCCAG
390 AGGGTTTAATTTATTAATTTATAAAACTATTCTGTTAAATCTGGTCCAACCGATTAAATTTCCAG
* *
2057337 GTAATGAAATGGGTTTTTAAGTTGAATTTTATTAAGCCGTGTTGTTTTTTAGTATGATTTTTAAG
455 GTAATGAAATGGATTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTTTAAG
2057402 TTC
520 TTC
* * *
2057405 GGTTCGAATGTCTGATTCTTTGTATTTATACATTGGGTTTTGTTGTATTTTTAATTTTGATTTTG
1 GGTTCGAATGTCCGATTCTTCGTATTTATACATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
*
2057470 CTTTCTTATTGGTTGGTGATACTAGAATTAAAAAAAAAT-TATTCTCTGTGTTTAGGGTTTTCGG
66 CTTTCTTATTGGTTGGTGATACTAGAATT--AAAAAAATGTATTCTCTGTGCTTAGGGTTTTCGG
2057534 TGTGTTCGACTATTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTACTGTTT
129 TGTGTTCGACTATTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTACTGTTT
2057599 TTGTAAATGGTTTAATTTGTTAGGAACTGATTTTAAGTTTTG-TTTTTTTTCTCCAGTTTTTGGT
194 TTGTAAATGGTTTAATTTGTTAGGAACTGATTTTAAGTTTTGTTTTTTTTTCTCCAGTTTTTGGT
2057663 CAATCCATTTCATTGCTTTCATTTCAGTTTTCTTCATCATTCTGAAGGTACAGAACACATGCTTT
259 CAATCCATTTCATTGCTTTCATTTCAGTTTTCTTCATCATTCTGAAGGTACAGAACACATGCTTT
* *
2057728 GTTACTGTTTATTTGTTGAAATCATTTGGTACTGTTTTTAAAGTATGGAATTTTGATGTCTAGTT
324 GTTACTGTTTATTTGTTGAAATCATTTGGTACTGCTTTTAAAGTATGGAATTTTGATGTCTAGCT
* * *
2057793 TAGGGTTTAATTTATTAATTTATAAAACTGTTCTGTTAAATGTGGTCCAGCCGATTAAATTTCCA
389 TAGGGTTTAATTTATTAATTTATAAAACTATTCTGTTAAATCTGGTCCAACCGATTAAATTTCCA
2057858 GGTAATGAAATGGATTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTTTAA
454 GGTAATGAAATGGATTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTTTAA
2057923 GTTC
519 GTTC
2057927 G
1 G
2057928 ATATATATAC
Statistics
Matches: 503, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
522 276 0.55
523 90 0.18
524 129 0.26
525 8 0.02
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (522 bp):
GGTTCGAATGTCCGATTCTTCGTATTTATACATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
CTTTCTTATTGGTTGGTGATACTAGAATTAAAAAAATGTATTCTCTGTGCTTAGGGTTTTCGGTG
TGTTCGACTATTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTACTGTTTTT
GTAAATGGTTTAATTTGTTAGGAACTGATTTTAAGTTTTGTTTTTTTTTCTCCAGTTTTTGGTCA
ATCCATTTCATTGCTTTCATTTCAGTTTTCTTCATCATTCTGAAGGTACAGAACACATGCTTTGT
TACTGTTTATTTGTTGAAATCATTTGGTACTGCTTTTAAAGTATGGAATTTTGATGTCTAGCTTA
GGGTTTAATTTATTAATTTATAAAACTATTCTGTTAAATCTGGTCCAACCGATTAAATTTCCAGG
TAATGAAATGGATTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTTTAAGT
TC
Found at i:2058653 original size:17 final size:17
Alignment explanation
Indices: 2058633--2058682 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
2058623 TTAATATCTA
2058633 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
*
2058650 TATAAGTTTGCT-AA--
1 TATAAGTTTTCTAAATT
2058664 -ATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
2058680 TAT
1 TAT
2058683 TTGTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
16 2 0.07
17 13 0.48
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:2058709 original size:15 final size:15
Alignment explanation
Indices: 2058674--2058712 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
2058664 ATAAGTTTTC
*
2058674 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
2058689 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
2058705 TAAATTTA
1 TAAATTTA
2058713 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:2058791 original size:61 final size:61
Alignment explanation
Indices: 2058644--2058792 Score: 190
Period size: 62 Copynumber: 2.4 Consensus size: 61
2058634 ATAAGTTTTC
* * * *
2058644 TAAATTTATAAGTTTGCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTATTAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTATTAGTAATAAAATTTATTAGTAT
** * *
2058705 TAAATTTACTTCGTTTTCTAAATAAGTGTTCTAAATTTGTTAGTAATAAATTTTATTAGTAT
1 TAAATTTA-TAAGTTTTCTAAATAAGTGTTCTAAATTTATTAGTAATAAAATTTATTAGTAT
* * *
2058767 TAATTTTATAAATTTTCTACATAAGT
1 TAAATTTATAAGTTTTCTAAATAAGT
2058793 TACATAATAC
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 22 0.30
62 52 0.70
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.50
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTATTAGTAATAAAATTTATTAGTAT
Found at i:2058818 original size:9 final size:9
Alignment explanation
Indices: 2058784--2058870 Score: 56
Period size: 9 Copynumber: 9.8 Consensus size: 9
2058774 ATAAATTTTC
*
2058784 TACATAAGT
1 TACATAACT
2058793 TACATAA--
1 TACATAACT
**
2058800 TACACCACT
1 TACATAACT
2058809 TACATAACT
1 TACATAACT
*
2058818 TACAAAACT
1 TACATAACT
*
2058827 TATATAA--
1 TACATAACT
2058834 TACATAACT
1 TACATAACT
*
2058843 TATATTTAAGCT
1 TACA--TAA-CT
*
2058855 TGCATAACT
1 TACATAACT
2058864 TACATAA
1 TACATAA
2058871 TAACTTACTT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
7 11 0.19
9 38 0.64
10 3 0.05
11 3 0.05
12 4 0.07
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:2058847 original size:16 final size:16
Alignment explanation
Indices: 2058784--2058844 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
2058774 ATAAATTTTC
*
2058784 TACATAAGTTACATAA
1 TACATAACTTACATAA
**
2058800 TACACCACTTACATAA
1 TACATAACTTACATAA
* *
2058816 CTTACAAAACTTATATAA
1 --TACATAACTTACATAA
2058834 TACATAACTTA
1 TACATAACTTA
2058845 TATTTAAGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 23 0.64
18 13 0.36
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:2058875 original size:12 final size:12
Alignment explanation
Indices: 2058858--2059044 Score: 64
Period size: 12 Copynumber: 17.4 Consensus size: 12
2058848 TTAAGCTTGC
2058858 ATAACTTACATA
1 ATAACTTACATA
2058870 ATAACTTAC-T-
1 ATAACTTACATA
*
2058880 -TAACTTATAT-
1 ATAACTTACATA
*
2058890 ATAA-TAACATA
1 ATAACTTACATA
*
2058901 ATAAATTACATA
1 ATAACTTACATA
*
2058913 AT-ACTT-TAT-
1 ATAACTTACATA
* *
2058922 GTTA--TA-ATA
1 ATAACTTACATA
*
2058931 CATAACTTATAT-
1 -ATAACTTACATA
*
2058943 ATAAGCTTGCAT-
1 ATAA-CTTACATA
2058955 A--ACTTACATA
1 ATAACTTACATA
2058965 ATAACTTACAT-
1 ATAACTTACATA
2058976 ATAA--TAGCATA
1 ATAACTTA-CATA
*
2058987 ATAAATTACATA
1 ATAACTTACATA
*
2058999 AT-ACTT-TAT-
1 ATAACTTACATA
*
2059008 ATAA-TAACATA
1 ATAACTTACATA
2059019 ATAACTT--A-A
1 ATAACTTACATA
*
2059028 ATAACTTATATA
1 ATAACTTACATA
2059040 ATAAC
1 ATAAC
2059045 ATAATAACTA
Statistics
Matches: 132, Mismatches: 17, Indels: 52
0.66 0.08 0.26
Matches are distributed among these distances:
8 3 0.02
9 27 0.20
10 21 0.16
11 31 0.23
12 46 0.35
13 4 0.03
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:2058981 original size:14 final size:12
Alignment explanation
Indices: 2058953--2059044 Score: 69
Period size: 12 Copynumber: 8.4 Consensus size: 12
2058943 ATAAGCTTGC
2058953 ATAACTTACATA
1 ATAACTTACATA
2058965 ATAACTTACAT-
1 ATAACTTACATA
2058976 ATAA--TAGCATA
1 ATAACTTA-CATA
*
2058987 ATAAATTACATA
1 ATAACTTACATA
*
2058999 AT-ACTT-TAT-
1 ATAACTTACATA
*
2059008 ATAA-TAACATA
1 ATAACTTACATA
2059019 ATAACTT--A-A
1 ATAACTTACATA
*
2059028 ATAACTTATATA
1 ATAACTTACATA
2059040 ATAAC
1 ATAAC
2059045 ATAATAACTA
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
9 13 0.20
10 9 0.14
11 16 0.25
12 24 0.38
13 2 0.03
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:2059019 original size:32 final size:32
Alignment explanation
Indices: 2058953--2059059 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 32
2058943 ATAAGCTTGC
* *
2058953 ATAACTTACATAATAACTTACATATAATAGCATA
1 ATAACTTACATAAT-ACTT-TATATAATAACATA
*
2058987 ATAAATTACATAATACTTTATATAATAACATA
1 ATAACTTACATAATACTTTATATAATAACATA
*
2059019 ATAACTTAAAT-A-AC-TTATATAATAACATA
1 ATAACTTACATAATACTTTATATAATAACATA
*
2059048 ATAACTAACATA
1 ATAACTTACATA
2059060 CAATATATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 24 0.37
30 2 0.03
31 1 0.02
32 21 0.32
33 4 0.06
34 13 0.20
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (32 bp):
ATAACTTACATAATACTTTATATAATAACATA
Found at i:2059037 original size:27 final size:27
Alignment explanation
Indices: 2059010--2059433 Score: 195
Period size: 27 Copynumber: 15.4 Consensus size: 27
2059000 TACTTTATAT
2059010 AATAACATA-ATAACTTAAATAACTTATA
1 AATAACATACATAACTTAAATAAC-T-TA
*
2059038 TAATAACATA-ATAAC-TAACAT-ACAATA
1 -AATAACATACATAACTTAA-ATAAC-TTA
* * **
2059065 TATAAACATATATAGAAACTTGCATAACTTA
1 AAT-AACATACAT---AACTTAAATAACTTA
* * * *
2059096 TATAATA-ACATAA--TACATAACCTA
1 AATAACATACATAACTTAAATAACTTA
* *
2059120 AATAACTTACATAAATTAAATAACTTA
1 AATAACATACATAACTTAAATAACTTA
* * *
2059147 CATAA-ATTAAATAACTTACATAACTTA
1 AATAACA-TACATAACTTAAATAACTTA
* * *
2059174 CATAACTTACATAAATTAAATAACTTACA
1 AATAACATACATAACTTAAATAACTT--A
* * * *
2059203 TAACTTACATTATACACAACTTACATAAATTA
1 -AA--TA-A-CATACATAACTTAAATAACTTA
* * * *
2059235 AATAACTTACATAACTTACATTAATTA
1 AATAACATACATAACTTAAATAACTTA
* * *
2059262 AATAACTTACATAACTTACATAAATTA
1 AATAACATACATAACTTAAATAACTTA
* *
2059289 AATAACTTACATAACTTACATAACTTA
1 AATAACATACATAACTTAAATAACTTA
* * * * *
2059316 CAT--TATACACAACTTACATAAATTA
1 AATAACATACATAACTTAAATAACTTA
* *
2059341 AATAACTTACATAACTTACATAACTTA
1 AATAACATACATAACTTAAATAACTTA
* * * *
2059368 CATAA-ATTAAATAACTTACATAACTTG
1 AATAACA-TACATAACTTAAATAACTTA
* * *
2059395 CATAACTTACATAAATTAAATAACTTA
1 AATAACATACATAACTTAAATAACTTA
* *
2059422 CATAACTTACAT
1 AATAACATACAT
2059434 TATACATAAC
Statistics
Matches: 315, Mismatches: 56, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
24 13 0.04
25 26 0.08
26 4 0.01
27 204 0.65
28 8 0.03
29 22 0.07
30 4 0.01
31 12 0.04
32 6 0.02
33 1 0.00
34 15 0.05
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.33
Consensus pattern (27 bp):
AATAACATACATAACTTAAATAACTTA
Found at i:2059133 original size:9 final size:9
Alignment explanation
Indices: 2059081--2059567 Score: 435
Period size: 9 Copynumber: 56.2 Consensus size: 9
2059071 CATATATAGA
*
2059081 AACTTGCAT
1 AACTTACAT
*
2059090 AACTTATAT
1 AACTTACAT
*
2059099 AA-TAACAT
1 AACTTACAT
2059107 AA--TACAT
1 AACTTACAT
* *
2059114 AACCTAAAT
1 AACTTACAT
2059123 AACTTACAT
1 AACTTACAT
* *
2059132 AAATTAAAT
1 AACTTACAT
2059141 AACTTACAT
1 AACTTACAT
* *
2059150 AAATTAAAT
1 AACTTACAT
2059159 AACTTACAT
1 AACTTACAT
2059168 AACTTACAT
1 AACTTACAT
2059177 AACTTACAT
1 AACTTACAT
* *
2059186 AAATTAAAT
1 AACTTACAT
2059195 AACTTACAT
1 AACTTACAT
2059204 AACTTACAT
1 AACTTACAT
* *
2059213 TA--TACAC
1 AACTTACAT
2059220 AACTTACAT
1 AACTTACAT
* *
2059229 AAATTAAAT
1 AACTTACAT
2059238 AACTTACAT
1 AACTTACAT
2059247 AACTTACATT
1 AACTTACA-T
*
2059257 AA-TTAAAT
1 AACTTACAT
2059265 AACTTACAT
1 AACTTACAT
2059274 AACTTACAT
1 AACTTACAT
* *
2059283 AAATTAAAT
1 AACTTACAT
2059292 AACTTACAT
1 AACTTACAT
2059301 AACTTACAT
1 AACTTACAT
2059310 AACTTACAT
1 AACTTACAT
* *
2059319 TA--TACAC
1 AACTTACAT
2059326 AACTTACAT
1 AACTTACAT
* *
2059335 AAATTAAAT
1 AACTTACAT
2059344 AACTTACAT
1 AACTTACAT
2059353 AACTTACAT
1 AACTTACAT
2059362 AACTTACAT
1 AACTTACAT
* *
2059371 AAATTAAAT
1 AACTTACAT
2059380 AACTTACAT
1 AACTTACAT
*
2059389 AACTTGCAT
1 AACTTACAT
2059398 AACTTACAT
1 AACTTACAT
* *
2059407 AAATTAAAT
1 AACTTACAT
2059416 AACTTACAT
1 AACTTACAT
2059425 AACTTACAT
1 AACTTACAT
*
2059434 TA--TACAT
1 AACTTACAT
*
2059441 AACCTT-CTT
1 AA-CTTACAT
*
2059450 AACTTTCAT
1 AACTTACAT
* *
2059459 TA--TACAC
1 AACTTACAT
*
2059466 AACTCACAT
1 AACTTACAT
2059475 AA-TTA-AT
1 AACTTACAT
* *
2059482 -ATTATACAC
1 AACT-TACAT
2059491 AACTTACAT
1 AACTTACAT
2059500 AA--TACAT
1 AACTTACAT
*
2059507 TACTTACAT
1 AACTTACAT
*
2059516 AACTTTCAT
1 AACTTACAT
*
2059525 TACTTACAGT
1 AACTTACA-T
2059535 -ACTTACAT
1 AACTTACAT
2059543 AA--TACAT
1 AACTTACAT
2059550 AA--TACAT
1 AACTTACAT
2059557 AACTTACAT
1 AACTTACAT
2059566 AA
1 AA
2059568 TACATAAAAA
Statistics
Matches: 383, Mismatches: 71, Indels: 48
0.76 0.14 0.10
Matches are distributed among these distances:
6 1 0.00
7 49 0.13
8 17 0.04
9 309 0.81
10 7 0.02
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:2059440 original size:106 final size:106
Alignment explanation
Indices: 2059122--2059442 Score: 444
Period size: 115 Copynumber: 2.9 Consensus size: 106
2059112 ATAACCTAAA
* *
2059122 TAACTTACATAAATTAAATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATA
1 TAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATA
* * *
2059187 AATTAAATAACTTACATAACTTACATTATACACAACTTACA
66 AATTAAATAACTTACATAACTTACATTATACATAAATTAAA
* * * * *
2059228 TAAATTAAATAACTTACATAACTTACATTAATTAAATAACTTACATAACTTACATAAATTAAATA
1 TAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATA
* *
2059293 ACTTACATAACTTACATAACTTACATTATACACAACTTACATAAATTAAA
66 AATTAAATAACTTACATAACTTACA-T-T-----A--TACATAAATTAAA
*
2059343 TAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTGCATAACTTACATA
1 TAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATA
2059408 AATTAAATAACTTACATAACTTACATTATACATAA
66 AATTAAATAACTTACATAACTTACATTATACATAA
2059443 CCTTCTTAAC
Statistics
Matches: 186, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
106 88 0.47
107 1 0.01
108 2 0.01
113 2 0.01
114 1 0.01
115 92 0.49
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.34
Consensus pattern (106 bp):
TAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATA
AATTAAATAACTTACATAACTTACATTATACATAAATTAAA
Found at i:2059453 original size:106 final size:106
Alignment explanation
Indices: 2059124--2059454 Score: 448
Period size: 106 Copynumber: 3.0 Consensus size: 106
2059114 AACCTAAATA
* * *
2059124 ACTTACATAAATTAAATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATAAA
1 ACTTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATAAA
*
2059189 TTAAATAACTTACATAACTTACATTATACACAACTTACATA
66 TTAAATAACTTACATAACTTACATTATACACAACTTACTTA
* * * * *
2059230 AATTAAATAACTTACATAACTTACATTAATTAAATAACTTACATAACTTACATAAATTAAATAAC
1 ACTTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATAAA
*
2059295 TTACATAACTTACATAACTTACATTATACACAACTTACATAAATTAAATA
66 TTAAATAACTTACATAACTTACATTATACACAACTTAC------T---TA
* *
2059345 ACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTGCATAACTTACATAAA
1 ACTTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATAAA
*
2059410 TTAAATAACTTACATAACTTACATTATACATAACCTT-CTTA
66 TTAAATAACTTACATAACTTACATTATACACAA-CTTACTTA
2059451 ACTT
1 ACTT
2059455 TCATTATACA
Statistics
Matches: 196, Mismatches: 19, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
106 100 0.51
109 1 0.01
115 92 0.47
116 3 0.02
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (106 bp):
ACTTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATAAA
TTAAATAACTTACATAACTTACATTATACACAACTTACTTA
Found at i:2059505 original size:66 final size:65
Alignment explanation
Indices: 2059269--2059574 Score: 224
Period size: 70 Copynumber: 4.5 Consensus size: 65
2059259 TTAAATAACT
* * * *
2059269 TACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATTA-TACACAACTTAC
1 TACATAA--TACATAACTTACATAA--TACATAACTTACATAACTTTCATTACTACACAACTCAC
2059333 ATAAA
62 AT-AA
* * * * * * * *
2059338 TTAAATAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTGCATAACTT
1 -TACATAA--TACATAACTTACATAA--TACATAACTTACATAACTTTCATTAC-TACACAACTC
2059403 ACATAAA
60 ACAT-AA
* * *
2059410 TTAAATAACTTACATAACTTACATTATACATAACCTT-CTTAACTTTCATTA-TACACAACTCAC
1 -TACATAA--TACATAACTTACATAATACATAA-CTTACATAACTTTCATTACTACACAACTCAC
2059473 ATAA
62 ATAA
* * ** *
2059477 TTA-ATATTATACACAACTTACATAATACATTACTTACATAACTTTCATTACTTACAGTACTTAC
1 -TACATA--ATACATAACTTACATAATACATAACTTACATAACTTTCATTAC-TACACAACTCAC
2059541 ATAA
62 ATAA
2059545 TACATAATACATAACTTACATAATACATAA
1 TACATAATACATAACTTACATAATACATAA
2059575 AAATATATCA
Statistics
Matches: 201, Mismatches: 26, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
65 3 0.01
66 58 0.29
67 7 0.03
68 28 0.14
70 63 0.31
71 2 0.01
72 40 0.20
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (65 bp):
TACATAATACATAACTTACATAATACATAACTTACATAACTTTCATTACTACACAACTCACATAA
Found at i:2059527 original size:18 final size:16
Alignment explanation
Indices: 2059492--2059572 Score: 76
Period size: 16 Copynumber: 4.9 Consensus size: 16
2059482 ATTATACACA
2059492 ACTTACATAATACATT
1 ACTTACATAATACATT
*
2059508 ACTTACATAACTTTCATT
1 ACTTACATAA--TACATT
*
2059526 ACTTACAGTACTTACA-T
1 ACTTACA-TA-ATACATT
* *
2059543 A-ATACATAATACATA
1 ACTTACATAATACATT
2059558 ACTTACATAATACAT
1 ACTTACATAATACAT
2059573 AAAAATATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
16 26 0.50
17 2 0.04
18 15 0.29
19 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.36
Consensus pattern (16 bp):
ACTTACATAATACATT
Found at i:2059550 original size:7 final size:7
Alignment explanation
Indices: 2059538--2059574 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
2059528 TTACAGTACT
2059538 TACATAA
1 TACATAA
2059545 TACATAA
1 TACATAA
2059552 TACATAA
1 TACATAA
2059559 CTTACATAA
1 --TACATAA
2059568 TACATAA
1 TACATAA
2059575 AAATATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 21 0.75
9 7 0.25
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:2061966 original size:19 final size:19
Alignment explanation
Indices: 2061930--2061988 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
2061920 ATTTTGAATT
* *
2061930 TTTTTTACATATTCTTTAGAA
1 TTTTTAACAT-TT-TTTAAAA
2061951 TTTTTAACATTTTTTAAAA
1 TTTTTAACATTTTTTAAAA
*
2061970 TTATTATA-ATTTTTTAAAA
1 TTTTTA-ACATTTTTTAAAA
2061989 ATATAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 22 0.65
20 3 0.09
21 9 0.26
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTAACATTTTTTAAAA
Found at i:2062137 original size:18 final size:18
Alignment explanation
Indices: 2062114--2062151 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2062104 TACCAATATG
2062114 TTATTTGAG-TTATTCGAA
1 TTATTT-AGTTTATTCGAA
*
2062132 TTATTTAGTTTATTTGAA
1 TTATTTAGTTTATTCGAA
2062150 TT
1 TT
2062152 GTAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (18 bp):
TTATTTAGTTTATTCGAA
Found at i:2070825 original size:24 final size:24
Alignment explanation
Indices: 2070780--2070826 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2070770 ATTACACCTT
*
2070780 ATATTACAGGATGACCGTAATGTG
1 ATATTACAGGATGACCGGAATGTG
**
2070804 ATATTACAGGATGGTCGGAATGT
1 ATATTACAGGATGACCGGAATGT
2070827 TGAAATCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (24 bp):
ATATTACAGGATGACCGGAATGTG
Found at i:2071468 original size:56 final size:61
Alignment explanation
Indices: 2071346--2071469 Score: 204
Period size: 56 Copynumber: 2.1 Consensus size: 61
2071336 TATCAAATAC
2071346 CTAAAATTACTCATAGCTCTTTTCCAACCCTTAAAATTAGGAGAATAATATGTTTCAGCGTA
1 CTAAAATTACTCATAGCTCTTTTCCAACCCTTAAAATTAGGAGAATAATA-GTTTCAGCGTA
2071408 CTAAAATTA-TCATAGCTC-TTTCCAACCCTT-AAA-TAGGAGAATAATA-TTTCAGCGTA
1 CTAAAATTACTCATAGCTCTTTTCCAACCCTTAAAATTAGGAGAATAATAGTTTCAGCGTA
2071464 CTAAAA
1 CTAAAA
2071470 CTCACGTTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
56 16 0.26
58 13 0.21
59 3 0.05
60 12 0.19
61 9 0.15
62 9 0.15
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (61 bp):
CTAAAATTACTCATAGCTCTTTTCCAACCCTTAAAATTAGGAGAATAATAGTTTCAGCGTA
Found at i:2091198 original size:22 final size:22
Alignment explanation
Indices: 2091156--2091199 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2091146 CCTAACGTAT
* *
2091156 AAAAATTAATTTATCTATTTAA
1 AAAAATTAATCTAACTATTTAA
2091178 AAAAATTCAATCTAACT-TTTAA
1 AAAAATT-AATCTAACTATTTAA
2091200 TTTAATAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATTAATCTAACTATTTAA
Found at i:2097027 original size:46 final size:46
Alignment explanation
Indices: 2096960--2097076 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
2096950 TTTGAGTACT
*
2096960 TCTGATCAAGTGACAAAGTGATAGGTGATAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTTAGCTACACTTA
2097006 TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTTAGCTACACTTA
*
2097052 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
2097077 TTCATACGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
44 12 0.17
45 5 0.07
46 52 0.75
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTTAGCTACACTTA
Found at i:2105605 original size:13 final size:13
Alignment explanation
Indices: 2105587--2105611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2105577 ATATGATATG
2105587 TTTTATTTTTTAT
1 TTTTATTTTTTAT
2105600 TTTTATTTTTTA
1 TTTTATTTTTTA
2105612 AAAGAGAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:2105895 original size:20 final size:21
Alignment explanation
Indices: 2105852--2105906 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
2105842 CTCTCTCAAC
2105852 AAAAATTACAAAATAATTTTT
1 AAAAATTACAAAATAATTTTT
2105873 -AAAATT-CAAAAT-ATGTTTAT
1 AAAAATTACAAAATAAT-TTT-T
*
2105893 AAAAATTCCAAAAT
1 AAAAATTACAAAAT
2105907 TTGTGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.07
19 9 0.30
20 7 0.23
21 6 0.20
22 6 0.20
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAATTACAAAATAATTTTT
Found at i:2106357 original size:3 final size:3
Alignment explanation
Indices: 2106349--2106379 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2106339 TTTGAAATTG
2106349 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2106380 ACCAACAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2114792 original size:17 final size:17
Alignment explanation
Indices: 2114770--2114803 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2114760 ATCCACTAAT
*
2114770 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2114787 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2114804 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2119431 original size:17 final size:17
Alignment explanation
Indices: 2119409--2119442 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2119399 ATCCACTAAT
*
2119409 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2119426 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2119443 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2143218 original size:20 final size:20
Alignment explanation
Indices: 2143179--2143218 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2143169 CCGTAAAATG
**
2143179 ATTTCTGGAAAATGTTTTAC
1 ATTTCTGGAAAATGACTTAC
*
2143199 ATTTCTGTAAAATGACTTAC
1 ATTTCTGGAAAATGACTTAC
2143219 TGGAAAATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
ATTTCTGGAAAATGACTTAC
Found at i:2143226 original size:35 final size:34
Alignment explanation
Indices: 2143166--2143231 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
2143156 AGTAAAATAT
*
2143166 TTTCCGTAAAATGATTTCTGGAAAATGTTTTACA
1 TTTCCGTAAAATGATTACTGGAAAATGTTTTACA
*
2143200 TTTCTGTAAAATGACTTACTGGAAAATGTTTT
1 TTTCCGTAAAATGA-TTACTGGAAAATGTTTT
2143232 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTCCGTAAAATGATTACTGGAAAATGTTTTACA
Found at i:2144417 original size:18 final size:18
Alignment explanation
Indices: 2144361--2144405 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2144351 GCTTCGAAAC
*
2144361 GGGAAAGGGAAGGAGAAG
1 GGGAAAGGGAAGGAGAAT
2144379 GGGAAAGGGAAGGAGAAT
1 GGGAAAGGGAAGGAGAAT
2144397 GGGAAAGGG
1 GGGAAAGGG
2144406 GAAAAGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (18 bp):
GGGAAAGGGAAGGAGAAT
Found at i:2156454 original size:13 final size:13
Alignment explanation
Indices: 2156436--2156460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2156426 TTTTGTTTCC
2156436 TTTTTCCTTTTTA
1 TTTTTCCTTTTTA
2156449 TTTTTCCTTTTT
1 TTTTTCCTTTTT
2156461 CCCGCCGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCCTTTTTA
Found at i:2159802 original size:17 final size:17
Alignment explanation
Indices: 2159777--2159816 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2159767 GTTAGTCTAC
* *
2159777 ATTAATTTTTAAATTTG
1 ATTATTTTTTAAATTTA
*
2159794 ATTATTTTTTCAATTTA
1 ATTATTTTTTAAATTTA
2159811 ATTATT
1 ATTATT
2159817 GAATTATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTATTTTTTAAATTTA
Found at i:2166001 original size:21 final size:21
Alignment explanation
Indices: 2165977--2166020 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2165967 TGGAGGGGAG
*
2165977 TGTGGAGGCGGTGGTGGAGAA
1 TGTGGAGGCGGTGGGGGAGAA
* * *
2165998 TGTGGTGGGGGTGGGGGTGAA
1 TGTGGAGGCGGTGGGGGAGAA
2166019 TG
1 TG
2166021 ATGTGGCGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.61, T:0.23
Consensus pattern (21 bp):
TGTGGAGGCGGTGGGGGAGAA
Found at i:2166026 original size:21 final size:21
Alignment explanation
Indices: 2165983--2166056 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
2165973 GGAGTGTGGA
* *
2165983 GGCGGTGGTGGAGAATG-TGGT
1 GGCGGTGGAGGTGAATGAT-GT
* *
2166004 GGGGGTGGGGGTGAATGATGT
1 GGCGGTGGAGGTGAATGATGT
*
2166025 GGCGGTGGAGGTGACTGATGT
1 GGCGGTGGAGGTGAATGATGT
*
2166046 GGTGGTGGAGG
1 GGCGGTGGAGG
2166057 GGAGTTATAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 44 0.98
22 1 0.02
ACGTcount: A:0.14, C:0.04, G:0.59, T:0.23
Consensus pattern (21 bp):
GGCGGTGGAGGTGAATGATGT
Found at i:2166205 original size:39 final size:39
Alignment explanation
Indices: 2166162--2166269 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 39
2166152 ATATTGGCGC
* *
2166162 AGGTGGTGGGGGTGAAGGGGGCGGTGGTGACGGATAAGT
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTGACGGATAAGT
* * * * *
2166201 AGGTGGCGGGGGTGAAGGTGGTGGAGGTGATGGATATGT
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTGACGGATAAGT
*
2166240 AGGGGGTGGGGGTGAAGGAGGTGGTGGTGA
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTGA
2166270 GGGCGGTGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.18, C:0.03, G:0.60, T:0.19
Consensus pattern (39 bp):
AGGTGGTGGGGGTGAAGGAGGTGGTGGTGACGGATAAGT
Found at i:2166268 original size:15 final size:15
Alignment explanation
Indices: 2166244--2166296 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2166234 ATATGTAGGG
*
2166244 GGTGGGGGTGAAGGA
1 GGTGGAGGTGAAGGA
* * *
2166259 GGTGGTGGTGAGGGC
1 GGTGGAGGTGAAGGA
* *
2166274 GGTGGAGGTGATGGT
1 GGTGGAGGTGAAGGA
2166289 GGTGGAGG
1 GGTGGAGG
2166297 AGGTGGAGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.13, C:0.02, G:0.66, T:0.19
Consensus pattern (15 bp):
GGTGGAGGTGAAGGA
Found at i:2166355 original size:21 final size:21
Alignment explanation
Indices: 2166331--2166376 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2166321 TGGTGGCGGA
2166331 GGCGAAGGAGGAGGAGGCGAG
1 GGCGAAGGAGGAGGAGGCGAG
** * *
2166352 GGCGGTGGTGGGGGAGGCGAG
1 GGCGAAGGAGGAGGAGGCGAG
2166373 GGCG
1 GGCG
2166377 GTGGTGGGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.67, T:0.04
Consensus pattern (21 bp):
GGCGAAGGAGGAGGAGGCGAG
Found at i:2166377 original size:21 final size:21
Alignment explanation
Indices: 2166343--2166389 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2166333 CGAAGGAGGA
2166343 GGAGGCGAGGGCGGTGGTGGG
1 GGAGGCGAGGGCGGTGGTGGG
2166364 GGAGGCGAGGGCGGTGGTGGG
1 GGAGGCGAGGGCGGTGGTGGG
2166385 GGAGG
1 GGAGG
2166390 TGAAAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.11, C:0.09, G:0.72, T:0.09
Consensus pattern (21 bp):
GGAGGCGAGGGCGGTGGTGGG
Found at i:2175964 original size:25 final size:25
Alignment explanation
Indices: 2175924--2175980 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
2175914 TATTAGATTG
* * * *
2175924 AAAATTAAATTGATTTTTTCTGTTA
1 AAAATTAAATTCATTTGTACCGTTA
*
2175949 AAAATTACATTCATTTGTACCGTTA
1 AAAATTAAATTCATTTGTACCGTTA
2175974 AAAATTA
1 AAAATTA
2175981 GTGTGGTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (25 bp):
AAAATTAAATTCATTTGTACCGTTA
Found at i:2185902 original size:20 final size:21
Alignment explanation
Indices: 2185861--2185904 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2185851 GACCCGGTCC
2185861 ATTTTTTTAATAAACACCAAAA
1 ATTTTTTTAATAAACA-CAAAA
2185883 ATTTATTTTAA-AAACA-AAAA
1 ATTT-TTTTAATAAACACAAAA
2185903 AT
1 AT
2185905 AAAAAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
22 9 0.43
23 6 0.29
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTTTTTAATAAACACAAAA
Found at i:2186654 original size:16 final size:17
Alignment explanation
Indices: 2186635--2186667 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2186625 TAATTCTTTG
2186635 TAATTAC-AAGAGAGTA
1 TAATTACTAAGAGAGTA
2186651 TAATTACTAAGAGAGTA
1 TAATTACTAAGAGAGTA
2186668 ATTGCACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (17 bp):
TAATTACTAAGAGAGTA
Found at i:2192313 original size:16 final size:16
Alignment explanation
Indices: 2192292--2192334 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2192282 AAAAAAGGAA
2192292 AGAAGGGAGAGAGGGG
1 AGAAGGGAGAGAGGGG
*
2192308 AGAAGGAAGAGAGGGG
1 AGAAGGGAGAGAGGGG
2192324 A-AAGGG-GAGAG
1 AGAAGGGAGAGAG
2192335 CTCCGGCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (16 bp):
AGAAGGGAGAGAGGGG
Found at i:2192329 original size:23 final size:24
Alignment explanation
Indices: 2192286--2192333 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
2192276 GAGAAAAAAA
*
2192286 AAGGAAAGAAGGGAGAGAGGGGAG
1 AAGGAAAGAAGGGAGAAAGGGGAG
2192310 AAGG-AAGAGAGGG-GAAAGGGGAG
1 AAGGAAAGA-AGGGAGAAAGGGGAG
2192333 A
1 A
2192334 GCTCCGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (24 bp):
AAGGAAAGAAGGGAGAAAGGGGAG
Found at i:2194539 original size:24 final size:24
Alignment explanation
Indices: 2194512--2194557 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2194502 GGGGCTTCCT
2194512 GTTAATTGCTCTTCGGAGCTACTC
1 GTTAATTGCTCTTCGGAGCTACTC
*
2194536 GTTAATTGCTCTTTGGAGCTAC
1 GTTAATTGCTCTTCGGAGCTAC
2194558 CCATTATAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (24 bp):
GTTAATTGCTCTTCGGAGCTACTC
Found at i:2196828 original size:27 final size:28
Alignment explanation
Indices: 2196779--2196847 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
2196769 TTTCCAAACA
*
2196779 CGACCTTGACCCTTTCTAGGGTTT-GAC
1 CGACCTTGACCTTTTCTAGGGTTTCGAC
* *
2196806 CGACCTTGGCCTTTTACTA-GGTTTCGGC
1 CGACCTTGACCTTTT-CTAGGGTTTCGAC
2196834 CGACCTTGACCTTT
1 CGACCTTGACCTTT
2196848 AGCGTATGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.13, C:0.30, G:0.22, T:0.35
Consensus pattern (28 bp):
CGACCTTGACCTTTTCTAGGGTTTCGAC
Found at i:2218791 original size:30 final size:30
Alignment explanation
Indices: 2218734--2218791 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2218724 AAGAACATAC
* *
2218734 AGAAAATAGTTTAAAACTTTACCAATTTAA
1 AGAAAATAGTTAAAAACTTTACAAATTTAA
2218764 AGAAAA-AGTTAAAAACTTTAACAAATTT
1 AGAAAATAGTTAAAAACTTT-ACAAATTT
2218792 CAGCATCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (30 bp):
AGAAAATAGTTAAAAACTTTACAAATTTAA
Found at i:2221402 original size:30 final size:30
Alignment explanation
Indices: 2221368--2221426 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2221358 TACAAGCTTT
2221368 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
* * * *
2221398 GGGGCAAAATTGTAATTTTGCTAAAGTTT
1 GGGGCAAAAGTGTAAATATGCAAAAGTTT
2221427 GAGTCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGCAAAAGTTTA
Found at i:2221779 original size:8 final size:8
Alignment explanation
Indices: 2221766--2221794 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2221756 CACTAGAGAT
2221766 CAGTGTTA
1 CAGTGTTA
2221774 CAGTGTTA
1 CAGTGTTA
2221782 CAGTGTTA
1 CAGTGTTA
2221790 CAGTG
1 CAGTG
2221795 AGTCTCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:2221908 original size:23 final size:23
Alignment explanation
Indices: 2221881--2221933 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2221871 AGTGTTATTG
2221881 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2221904 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2221927 ATCAGTG
1 ATCAGTG
2221934 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2222974 original size:2 final size:2
Alignment explanation
Indices: 2222969--2223002 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2222959 ATGACATATA
2222969 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2223003 ATAATAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2224580 original size:50 final size:50
Alignment explanation
Indices: 2224465--2224700 Score: 297
Period size: 50 Copynumber: 4.8 Consensus size: 50
2224455 GATCATAACA
* * ** *
2224465 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
2224516 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
2224566 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCA--TCGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
2224614 TG-----GCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
2224659 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2224701 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
43 35 0.22
45 4 0.03
48 5 0.03
50 83 0.52
51 32 0.20
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:2224682 original size:93 final size:93
Alignment explanation
Indices: 2224523--2224700 Score: 302
Period size: 93 Copynumber: 1.9 Consensus size: 93
2224513 CGGTGCCCAT
* *
2224523 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACA
2224588 TGGTCTTACATGGGACCTCTCATCGTTG
66 TGGTCTTACATGGGACCTCTCATCGTTG
* * * *
2224616 GCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATCTTGGTGCCAATGCCATGTCCCAGACA
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACA
2224681 TGGTCTTACATGGGACCTCT
66 TGGTCTTACATGGGACCTCT
2224701 TTACCCAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (93 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACA
TGGTCTTACATGGGACCTCTCATCGTTG
Found at i:2225073 original size:30 final size:30
Alignment explanation
Indices: 2225038--2225095 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2225028 CCTCGACTCT
*
2225038 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTGCAAAATTACAATTTTGCCCCTA
* *
2225068 AACTTTTGCATAATTACATTTTTGCCCC
1 AACTTTTGCAAAATTACAATTTTGCCCC
2225096 AAAGCTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTGCCCCTA
Found at i:2228882 original size:12 final size:12
Alignment explanation
Indices: 2228867--2228897 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2228857 TTCTCTTTTA
2228867 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
2228879 TTTTTCTTTCGC
1 TTTTTCTTTCCC
2228891 TTTTTCT
1 TTTTTCT
2228898 CCCCTGCTTC
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:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:2229508 original size:13 final size:15
Alignment explanation
Indices: 2229479--2229511 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2229469 GGTTAATAAT
2229479 TATAATAATTATATG
1 TATAATAATTATATG
2229494 TATAAT-ATT-TATG
1 TATAATAATTATATG
2229507 TATAA
1 TATAA
2229512 CTTAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TATAATAATTATATG
Found at i:2230110 original size:28 final size:28
Alignment explanation
Indices: 2230079--2230133 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2230069 TTAAAACTAT
*
2230079 TTAATAATTATTAAAAACTCGGAATAAC
1 TTAATAATTATTAAAAACTCAGAATAAC
*
2230107 TTAATAATTATTAAAAATTCAGAATAA
1 TTAATAATTATTAAAAACTCAGAATAA
2230134 TAAAATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (28 bp):
TTAATAATTATTAAAAACTCAGAATAAC
Found at i:2230140 original size:28 final size:28
Alignment explanation
Indices: 2230081--2230142 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2230071 AAAACTATTT
* *
2230081 AATAATTATTAAAAACTCGGAATAACTT
1 AATAATTATTAAAAACTCAGAATAACTA
*
2230109 AATAATTATTAAAAATTCAGAATAA-TAA
1 AATAATTATTAAAAACTCAGAATAACT-A
2230137 AATAAT
1 AATAAT
2230143 GAAAGCTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.32
Consensus pattern (28 bp):
AATAATTATTAAAAACTCAGAATAACTA
Found at i:2242851 original size:21 final size:23
Alignment explanation
Indices: 2242827--2242879 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2242817 TATAACTCTA
2242827 AAAATAAAAATA-TATTT-TAAT
1 AAAATAAAAATATTATTTATAAT
*
2242848 AAAA-ACAAAATATTTTTTATAAT
1 AAAATA-AAAATATTATTTATAAT
2242871 AAAATAAAA
1 AAAATAAAA
2242880 TCTATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 10 0.37
22 4 0.15
23 11 0.41
24 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATAAAAATATTATTTATAAT
Found at i:2253806 original size:44 final size:44
Alignment explanation
Indices: 2253743--2253831 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
2253733 CATATCTTGG
*
2253743 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATGACTTTAATAT
1 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATAACTTTAATAT
2253787 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATAACTTTAATAT
1 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATAACTTTAATAT
2253831 T
1 T
2253832 CTAACTGGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (44 bp):
TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATAACTTTAATAT
Found at i:2256417 original size:14 final size:14
Alignment explanation
Indices: 2256394--2256433 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2256384 ATAGAAAAGT
*
2256394 AAAATATTTTTCCG
1 AAAATATTTTACCG
* *
2256408 AAATTATTTTACGG
1 AAAATATTTTACCG
2256422 AAAATATTTTAC
1 AAAATATTTTAC
2256434 TGACAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (14 bp):
AAAATATTTTACCG
Found at i:2256425 original size:34 final size:35
Alignment explanation
Indices: 2256359--2256425 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
2256349 AAAACATCAG
*
2256359 AAAATATTTTTCAGTAAATCATTTTATAGAAAAGT
1 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
* * *
2256394 AAAATATTTTTCCG-AAATTATTTTACGGAAAA
1 AAAATATTTTTCAGTAAATCATTTTACAGAAAA
2256426 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (35 bp):
AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
Found at i:2257048 original size:15 final size:16
Alignment explanation
Indices: 2257006--2257049 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2256996 TTTAATAGAG
*
2257006 TCGAGTAAAATGAAAT
1 TCGAGTAAAATTAAAT
**
2257022 TCGAGTCGAATTAAA-
1 TCGAGTAAAATTAAAT
2257037 TCGAGTAAAATTA
1 TCGAGTAAAATTA
2257050 TTTGAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (16 bp):
TCGAGTAAAATTAAAT
Found at i:2264811 original size:16 final size:15
Alignment explanation
Indices: 2264786--2264815 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2264776 ATCAATTACA
2264786 GAAAAATTCATATTC
1 GAAAAATTCATATTC
2264801 GAAATAATTCATATT
1 GAAA-AATTCATATT
2264816 GTCCCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (15 bp):
GAAAAATTCATATTC
Found at i:2269753 original size:21 final size:21
Alignment explanation
Indices: 2269729--2269769 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2269719 AATTTTTATA
*
2269729 TTTTTATTTTTAAAATTTTAC
1 TTTTAATTTTTAAAATTTTAC
2269750 TTTTAATTTTTAAAATTTTA
1 TTTTAATTTTTAAAATTTTA
2269770 AAATTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAATTTTTAAAATTTTAC
Found at i:2269953 original size:7 final size:7
Alignment explanation
Indices: 2269941--2269971 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2269931 ATATCAAAAA
2269941 ATTAAAT
1 ATTAAAT
2269948 ATTAAAT
1 ATTAAAT
2269955 ATTAAAT
1 ATTAAAT
2269962 ATTAAA-
1 ATTAAAT
2269968 ATTA
1 ATTA
2269972 TGAAGAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTAAAT
Found at i:2269969 original size:22 final size:20
Alignment explanation
Indices: 2269919--2269971 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
2269909 ATAGTTACAC
2269919 TTAAAATTTAGAATATCAAAAAA
1 TTAAAA-TTA-AATATC-AAAAA
* *
2269942 TTAAATATTAAATATTAAATA
1 TTAAA-ATTAAATATCAAAAA
2269963 TTAAAATTA
1 TTAAAATTA
2269972 TGAAGAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 5 0.19
23 8 0.30
24 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTAAAATTAAATATCAAAAA
Found at i:2274243 original size:28 final size:28
Alignment explanation
Indices: 2274197--2274322 Score: 155
Period size: 28 Copynumber: 4.5 Consensus size: 28
2274187 TGACTTTCGA
*
2274197 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
2274225 CGCTAAATGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
2274253 CACTAAGGGTG-GTAGTTTAATGGCAAAG
1 CACTAAGTGTGCG-AGTTTAATTGTAAAG
* * *
2274281 CACTAAGTGTGCGAGTTTGATTATTAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
2274309 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
2274323 ACTTATTAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.01
28 80 0.98
29 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:2275069 original size:46 final size:46
Alignment explanation
Indices: 2274995--2275123 Score: 131
Period size: 47 Copynumber: 2.8 Consensus size: 46
2274985 TATTAATGCA
* * * * *
2274995 TATGCTTTAATG--GTCCAAAATGTGGTATATGTTCATGT-AATTTT
1 TATGCTTAAATGCTGTCCAAATTGTTGTATATATGC-TGTCAATTTT
2275039 TATGCTTAAATGCTGTCCAAATTGTTGTATATATGCTGTCCAATTTT
1 TATGCTTAAATGCTGTCCAAATTGTTGTATATATGCTGT-CAATTTT
* * *
2275086 TATGCTAAAATGCTG-CTAAATTTGATGTATATATGCTG
1 TATGCTTAAATGCTGTCCAAA-TTGTTGTATATATGCTG
2275124 CCCAAATTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
44 11 0.15
45 3 0.04
46 22 0.31
47 36 0.50
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (46 bp):
TATGCTTAAATGCTGTCCAAATTGTTGTATATATGCTGTCAATTTT
Found at i:2275074 original size:23 final size:23
Alignment explanation
Indices: 2275048--2275151 Score: 95
Period size: 23 Copynumber: 4.5 Consensus size: 23
2275038 TTATGCTTAA
2275048 ATGCTGTCCAAATTGTTGTATAT
1 ATGCTGTCCAAATTGTTGTATAT
* * *
2275071 ATGCTGTCCAATTTTTATGCTA-AA
1 ATGCTGTCCAAATTGT-TG-TATAT
* *
2275095 ATGCTG-CTAAATTTGATGTATAT
1 ATGCTGTCCAAA-TTGTTGTATAT
* * *
2275118 ATGCTGCCCAAATTATTGTATAC
1 ATGCTGTCCAAATTGTTGTATAT
2275141 ATGCTGTCCAA
1 ATGCTGTCCAA
2275152 TTTTTGGTGT
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
22 2 0.03
23 44 0.70
24 15 0.24
25 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (23 bp):
ATGCTGTCCAAATTGTTGTATAT
Found at i:2275097 original size:47 final size:47
Alignment explanation
Indices: 2275033--2275128 Score: 140
Period size: 47 Copynumber: 2.0 Consensus size: 47
2275023 ATGTTCATGT
* * *
2275033 AATTTTTATGCTTAAATGCTGTCCAAA-TTGTTGTATATATGCTGTCC
1 AATTTTTATGCTAAAATGCTG-CCAAATTTGATGTATATATGCTGCCC
*
2275080 AATTTTTATGCTAAAATGCTGCTAAATTTGATGTATATATGCTGCCC
1 AATTTTTATGCTAAAATGCTGCCAAATTTGATGTATATATGCTGCCC
2275127 AA
1 AA
2275129 ATTATTGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 4 0.09
47 40 0.91
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (47 bp):
AATTTTTATGCTAAAATGCTGCCAAATTTGATGTATATATGCTGCCC
Found at i:2285395 original size:74 final size:74
Alignment explanation
Indices: 2285274--2285421 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
2285264 CAGAATCAGC
*
2285274 GTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATGTATTGATGCTTCGTATCATTTGGCA
1 GTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCGTATCATTTGGCA
2285339 TCCACCCAT
66 TCCACCCAT
* * *
2285348 GTGTAGTTATTTTTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTTATCATTTGGCA
1 GTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCGTATCATTTGGCA
2285413 TCCACCCAT
66 TCCACCCAT
2285422 TTCGCCGCCG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (74 bp):
GTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCGTATCATTTGGCA
TCCACCCAT
Found at i:2286550 original size:23 final size:23
Alignment explanation
Indices: 2286524--2286579 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2286514 TTTGGTGCTG
* *
2286524 TTTTGGTGCTGTTATAG-GTGTCA
1 TTTTGGTGCTGCTAT-GTGTGCCA
* *
2286547 TTTTGTTGCTGCTGTGTGTGCCA
1 TTTTGGTGCTGCTATGTGTGCCA
2286570 TTTTGGTGCT
1 TTTTGGTGCT
2286580 ATCAATGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.07, C:0.12, G:0.30, T:0.50
Consensus pattern (23 bp):
TTTTGGTGCTGCTATGTGTGCCA
Found at i:2306963 original size:24 final size:24
Alignment explanation
Indices: 2306936--2306994 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
2306926 CCCATCAGCT
*
2306936 CCTCCTCCTTCTACCACTCCATCC
1 CCTCCTCCTTCTACCACTCCATCA
* * *
2306960 CCTCCTCCTCCTTCCACTTCATCA
1 CCTCCTCCTTCTACCACTCCATCA
*
2306984 CCTCCGCCTTC
1 CCTCCTCCTTC
2306995 ATCCTCTGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.10, C:0.58, G:0.02, T:0.31
Consensus pattern (24 bp):
CCTCCTCCTTCTACCACTCCATCA
Found at i:2307172 original size:36 final size:36
Alignment explanation
Indices: 2307083--2307175 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
2307073 CTCATCAACA
* * * * *
2307083 CCATCTCCGCCGCCGCCACCGAGGAGTCCCGGTACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
2307119 GCATCTCCACCACCGCCTCCGAGGAATTCCGGGACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
2307155 CCATCTCCTCCTCCGCCTCCG
1 CCATCTCCACCACCGCCTCCG
2307176 TCTGATTCCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.14, C:0.48, G:0.20, T:0.17
Consensus pattern (36 bp):
CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
Found at i:2349062 original size:3 final size:3
Alignment explanation
Indices: 2349054--2349091 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2349044 TTATTTTGCT
2349054 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2349092 GTTCTCACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2377381 original size:20 final size:20
Alignment explanation
Indices: 2377356--2377395 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2377346 GCTAAGCACA
2377356 CAACATGATCGACGAAATAC
1 CAACATGATCGACGAAATAC
2377376 CAACATGATCGACGAAATAC
1 CAACATGATCGACGAAATAC
2377396 TCCAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (20 bp):
CAACATGATCGACGAAATAC
Found at i:2380176 original size:48 final size:48
Alignment explanation
Indices: 2380116--2380211 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2380106 AAAACAACCT
2380116 CAAATCGAATTTAAAAGAATTAACCTACATAGCTAATACAACTTTTTG
1 CAAATCGAATTTAAAAGAATTAACCTACATAGCTAATACAACTTTTTG
2380164 CAAATCGAATTTAAAAGAATTAACCTACATAGCTAATACAACTTTTTG
1 CAAATCGAATTTAAAAGAATTAACCTACATAGCTAATACAACTTTTTG
2380212 GACACCCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (48 bp):
CAAATCGAATTTAAAAGAATTAACCTACATAGCTAATACAACTTTTTG
Found at i:2380378 original size:18 final size:18
Alignment explanation
Indices: 2380357--2380404 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
2380347 TAAAAAACAA
* *
2380357 ATCAATTTTTATATTTTT
1 ATCAATTTTAATATTATT
*
2380375 ATCAAATTTAAATATTATT
1 ATC-AATTTTAATATTATT
2380394 A-CAATTTTAAT
1 ATCAATTTTAAT
2380405 TATGTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 13 0.52
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
ATCAATTTTAATATTATT
Found at i:2381328 original size:8 final size:8
Alignment explanation
Indices: 2381315--2381341 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2381305 ATACAAAATT
2381315 AATTTTAA
1 AATTTTAA
2381323 AATTTTAA
1 AATTTTAA
2381331 AATTTTAA
1 AATTTTAA
2381339 AAT
1 AAT
2381342 AATATAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:2381664 original size:3 final size:3
Alignment explanation
Indices: 2381658--2381690 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2381648 AAGGAAGGAA
2381658 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2381691 GTGAACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2394639 original size:24 final size:24
Alignment explanation
Indices: 2394612--2394663 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2394602 TTAGTAAGTC
*
2394612 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2394636 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2394660 AAAT
1 AAAT
2394664 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2396604 original size:24 final size:24
Alignment explanation
Indices: 2396577--2396628 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2396567 TTAGTAAGTC
*
2396577 AAATAAATCATACTAATAAATGCT
1 AAATAAATCATACTAATAAATACT
* *
2396601 AAATATATTATACTAATAAATACT
1 AAATAAATCATACTAATAAATACT
2396625 AAAT
1 AAAT
2396629 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATCATACTAATAAATACT
Found at i:2402350 original size:42 final size:42
Alignment explanation
Indices: 2402303--2402386 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
2402293 TGAAATATGA
2402303 TAATTGGTTTAGCAAGATTGAAAAGATGGAGGTGCACGTGGG
1 TAATTGGTTTAGCAAGATTGAAAAGATGGAGGTGCACGTGGG
2402345 TAATTGGTTTAGCAAGATTGAAAAGATGGAGGTGCACGTGGG
1 TAATTGGTTTAGCAAGATTGAAAAGATGGAGGTGCACGTGGG
2402387 ACTTCCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.07, G:0.36, T:0.26
Consensus pattern (42 bp):
TAATTGGTTTAGCAAGATTGAAAAGATGGAGGTGCACGTGGG
Found at i:2403516 original size:60 final size:55
Alignment explanation
Indices: 2403389--2403542 Score: 179
Period size: 53 Copynumber: 2.8 Consensus size: 55
2403379 TTTCTACCTA
*
2403389 AACTTGACACTTTTTCCTAATTTGGTATCTAAA-CTTTTTTTGGCCCAATTTGGT
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACCTTTTTTTGGCCCAATTTGGT
* *
2403443 -ACTTGACACTTTTTCCTAATTTGGCACCTAAACCATTTTTTGGCCCAATTTTGTATGT
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACCTTTTTTTGGCCCAA-TTTG---GT
* * * *
2403501 CAACTTGGCATTTTTTTCTAATTTAGTACCT-AACCTTTTTTT
1 -AACTTGACACTTTTTCCTAATTTGGTACCTAAACCTTTTTTT
2403543 TTAGGTTCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
53 30 0.36
54 14 0.17
55 4 0.05
58 2 0.02
59 10 0.12
60 24 0.29
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (55 bp):
AACTTGACACTTTTTCCTAATTTGGTACCTAAACCTTTTTTTGGCCCAATTTGGT
Found at i:2404031 original size:32 final size:33
Alignment explanation
Indices: 2403995--2404056 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
2403985 TAGACCCAAA
*
2403995 AAATTTAAGTA-CTAATTTAA-AAAAAATATATT
1 AAATTTAAGTATC-AAATTAAGAAAAAATATATT
2404027 AAATTTAAGTATCAAATTAAGAAAAAATAT
1 AAATTTAAGTATCAAATTAAGAAAAAATAT
2404057 CAAGTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (33 bp):
AAATTTAAGTATCAAATTAAGAAAAAATATATT
Found at i:2404675 original size:30 final size:32
Alignment explanation
Indices: 2404619--2404678 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2404609 TTTATTCTAA
*
2404619 ATTTTTAAAATTTTATGAACTTTTTAATTTCT
1 ATTTTGAAAATTTTATGAACTTTTTAATTTCT
*
2404651 ATTTTGAATATTTTAT-AA-TTTTTAATTT
1 ATTTTGAAAATTTTATGAACTTTTTAATTT
2404679 ATTTGTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
32 14 0.54
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (32 bp):
ATTTTGAAAATTTTATGAACTTTTTAATTTCT
Found at i:2409240 original size:18 final size:18
Alignment explanation
Indices: 2409207--2409241 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2409197 TCATCAATGG
* *
2409207 CGTCATCACCTTCCTCAT
1 CGTCATCAACTACCTCAT
2409225 CGTCATCAACTACCTCA
1 CGTCATCAACTACCTCA
2409242 GCTTCTTATG
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:0.23, C:0.43, G:0.06, T:0.29
Consensus pattern (18 bp):
CGTCATCAACTACCTCAT
Found at i:2428380 original size:13 final size:13
Alignment explanation
Indices: 2428362--2428388 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2428352 GCAAGTAGAC
2428362 TATGGTTCAAGCT
1 TATGGTTCAAGCT
2428375 TATGGTTCAAGCT
1 TATGGTTCAAGCT
2428388 T
1 T
2428389 CTTTCATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (13 bp):
TATGGTTCAAGCT
Found at i:2428758 original size:20 final size:20
Alignment explanation
Indices: 2428733--2428772 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2428723 AATTTTTGTG
2428733 TAAAACTAAAAGGAAAATAC
1 TAAAACTAAAAGGAAAATAC
2428753 TAAAACTAAAAGGAAAATAC
1 TAAAACTAAAAGGAAAATAC
2428773 ACTATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (20 bp):
TAAAACTAAAAGGAAAATAC
Found at i:2431837 original size:16 final size:16
Alignment explanation
Indices: 2431816--2431854 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
2431806 AATCTTACTC
2431816 TATATTTATA-TATAT
1 TATATTTATATTATAT
2431831 ATATATTTATATTATAT
1 -TATATTTATATTATAT
2431848 TATATTT
1 TATATTT
2431855 GCTTGGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTTATATTATAT
Found at i:2448856 original size:10 final size:10
Alignment explanation
Indices: 2448841--2448868 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2448831 GTCTCTTTCT
2448841 TCTCTCTCCC
1 TCTCTCTCCC
2448851 TCTCTCTCCC
1 TCTCTCTCCC
2448861 TCTCTCTC
1 TCTCTCTC
2448869 TCCCCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (10 bp):
TCTCTCTCCC
Found at i:2448858 original size:12 final size:11
Alignment explanation
Indices: 2448841--2448873 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
2448831 GTCTCTTTCT
2448841 TCTCTCT-CCC
1 TCTCTCTCCCC
2448851 TCTCTCTCCCTC
1 TCTCTCTCCC-C
2448863 TCTCTCTCCCC
1 TCTCTCTCCCC
2448874 GTGTTTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 3 0.14
12 11 0.52
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (11 bp):
TCTCTCTCCCC
Found at i:2453075 original size:9 final size:9
Alignment explanation
Indices: 2453050--2453079 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2453040 ATCATTAGCC
2453050 TAAGTTAAT
1 TAAGTTAAT
2453059 TAAGGTTAAT
1 TAA-GTTAAT
2453069 TAAGTTAAT
1 TAAGTTAAT
2453078 TA
1 TA
2453080 TGATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:2453089 original size:19 final size:19
Alignment explanation
Indices: 2453050--2453089 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2453040 ATCATTAGCC
*
2453050 TAAGTTAATTAAGGTTAAT
1 TAAGTTAATTAAGATTAAT
* *
2453069 TAAGTTAATTATGATTTAT
1 TAAGTTAATTAAGATTAAT
2453088 TA
1 TA
2453090 TATATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (19 bp):
TAAGTTAATTAAGATTAAT
Found at i:2456735 original size:18 final size:18
Alignment explanation
Indices: 2456714--2456748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2456704 AAAAAATATT
2456714 TATTTTATATTATTTTAA
1 TATTTTATATTATTTTAA
* *
2456732 TATTTTTTATTTTTTTA
1 TATTTTATATTATTTTA
2456749 TTTATTGAAA
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTATATTATTTTAA
Found at i:2470626 original size:13 final size:11
Alignment explanation
Indices: 2470599--2470624 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2470589 ATACATATGG
2470599 TATAATGTTTA
1 TATAATGTTTA
2470610 TATAATGTTTA
1 TATAATGTTTA
2470621 TATA
1 TATA
2470625 TATTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TATAATGTTTA
Found at i:2483612 original size:21 final size:21
Alignment explanation
Indices: 2483586--2483637 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2483576 CAGTGGTGGT
* *
2483586 GGTGAGGTTAGTTACTGTAAC
1 GGTGAGATTAGATACTGTAAC
* *
2483607 GGTGAGATTGGATACTGTAGC
1 GGTGAGATTAGATACTGTAAC
2483628 GGTGAGATTA
1 GGTGAGATTA
2483638 AAAACAATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.37, T:0.31
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAAC
Found at i:2484574 original size:10 final size:10
Alignment explanation
Indices: 2484542--2484576 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2484532 TTAACTTTTT
*
2484542 AAATTTAAAA
1 AAATATAAAA
2484552 AAA-ATAAAA
1 AAATATAAAA
2484561 AAATATAAAA
1 AAATATAAAA
2484571 AAATAT
1 AAATAT
2484577 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATATAAAA
Found at i:2496552 original size:21 final size:19
Alignment explanation
Indices: 2496528--2496581 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 19
2496518 TTTTTAATTA
2496528 AATTTTAAATAATATATTTTT
1 AATTTTAAATAAT-TA-TTTT
*
2496549 AATTATTTAATTAATTATTTT
1 AA-T-TTTAAATAATTATTTT
2496570 AATTGTTAAATA
1 AATT-TTAAATA
2496582 TAATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.04
20 7 0.25
21 8 0.29
22 3 0.11
23 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTTAAATAATTATTTT
Found at i:2496564 original size:12 final size:12
Alignment explanation
Indices: 2496520--2496573 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 12
2496510 GGCTTGATTT
*
2496520 TTTAATTAAAT-
1 TTTAATTAATTA
*
2496531 TTTAAATAATATA
1 TTTAATTAAT-TA
2496544 TTT--TTAATTA
1 TTTAATTAATTA
2496554 TTTAATTAATTA
1 TTTAATTAATTA
2496566 TTTTAATT
1 -TTTAATT
2496574 GTTAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 5 0.14
11 12 0.34
12 8 0.23
13 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAATTAATTA
Found at i:2496585 original size:22 final size:23
Alignment explanation
Indices: 2496536--2496587 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
2496526 TAAATTTTAA
*
2496536 ATAATATATTTTTAATTATTTAAT
1 ATAAT-TATTTTTAATTATTAAAT
*
2496560 -TAATTA-TTTTAATTGTTAAAT
1 ATAATTATTTTTAATTATTAAAT
2496581 ATAATTA
1 ATAATTA
2496588 AAATATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 13 0.52
22 8 0.32
23 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATAATTATTTTTAATTATTAAAT
Found at i:2497143 original size:18 final size:19
Alignment explanation
Indices: 2497108--2497145 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2497098 GTAGATCAAT
* *
2497108 AAAATTTTAATAATATTAA
1 AAAATATTAATAAAATTAA
2497127 AAAATATTAA-AAAATTAA
1 AAAATATTAATAAAATTAA
2497145 A
1 A
2497146 TCATAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATTAATAAAATTAA
Found at i:2497668 original size:23 final size:24
Alignment explanation
Indices: 2497626--2497673 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2497616 CAATTTTTTA
2497626 ATTATTAATAATTATAAATTTAAT
1 ATTATTAATAATTATAAATTTAAT
* *
2497650 ATTATT-ATAATTGTTAATTTAAT
1 ATTATTAATAATTATAAATTTAAT
2497673 A
1 A
2497674 ATATGTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTATTAATAATTATAAATTTAAT
Found at i:2514370 original size:51 final size:51
Alignment explanation
Indices: 2514312--2514493 Score: 183
Period size: 51 Copynumber: 3.6 Consensus size: 51
2514302 GTTCACATAA
* * *
2514312 TAGCCTGCACATAGTACTACACATGAGA-CCATTACCATCCGATACATGTAG
1 TAGCCTGCACATAGTACTACACATGTGACCCA-TACCATCCGGTACACGTAG
* * * * * * *
2514363 TAGCCTGCATATAGTACTACAC-TCGTGATCGAAACTATCCGGTACGCATAG
1 TAGCCTGCACATAGTACTACACAT-GTGACCCATACCATCCGGTACACGTAG
* *
2514414 TAGCCTGCATATAGTACTACACATGCGACCCAT--CATTCCGGTACACGTAG
1 TAGCCTGCACATAGTACTACACATGTGACCCATACCA-TCCGGTACACGTAG
* *
2514464 TAGCCTGCACATAGTACGACACACGTGACC
1 TAGCCTGCACATAGTACTACACATGTGACC
2514494 ATCGCTTTCA
Statistics
Matches: 107, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 39 0.36
51 64 0.60
52 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (51 bp):
TAGCCTGCACATAGTACTACACATGTGACCCATACCATCCGGTACACGTAG
Found at i:2514491 original size:101 final size:101
Alignment explanation
Indices: 2514307--2514491 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 101
2514297 GTTCGGTTCA
*
2514307 CATAATAGCCTGCACATAGTACTACACATGAGACCATTACCATCCGATACATGTAGTAGCCTGCA
1 CATAATAGCCTGCACATAGTACTACACATGAGACCATTA-CATCCGATACACGTAGTAGCCTGCA
* * *
2514372 TATAGTACTACACTCGTGATCGAAACTATCCGGTACG
65 CATAGTACGACACACGTGATCGAAACTATCCGGTACG
* * * *
2514409 CATAGTAGCCTGCATATAGTACTACACATGCGACCCA-T-CATTCCGGTACACGTAGTAGCCTGC
1 CATAATAGCCTGCACATAGTACTACACATGAGA-CCATTACA-TCCGATACACGTAGTAGCCTGC
2514472 ACATAGTACGACACACGTGA
64 ACATAGTACGACACACGTGA
2514492 CCATCGCTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 2 0.03
101 37 0.51
102 31 0.42
103 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAATAGCCTGCACATAGTACTACACATGAGACCATTACATCCGATACACGTAGTAGCCTGCAC
ATAGTACGACACACGTGATCGAAACTATCCGGTACG
Found at i:2533369 original size:30 final size:30
Alignment explanation
Indices: 2533329--2533440 Score: 179
Period size: 30 Copynumber: 3.7 Consensus size: 30
2533319 AATATCTCGG
2533329 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
*
2533359 TACTCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
2533389 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
2533419 TACCCATATATTTGATTTTCCA
1 TACCCATATCTTTGACTTTCCA
2533441 TAAATATGGA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.46
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTGA
Found at i:2533430 original size:15 final size:15
Alignment explanation
Indices: 2533329--2533434 Score: 65
Period size: 15 Copynumber: 7.1 Consensus size: 15
2533319 AATATCTCGG
*
2533329 TACCCATATCTTTGA
1 TACCCATATATTTGA
**
2533344 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
* *
2533359 TACTCATATCTTTGA
1 TACCCATATATTTGA
**
2533374 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
*
2533389 TACCCATATCTTTGA
1 TACCCATATATTTGA
** *
2533404 CTTTCTAT-TATTTGA
1 -TACCCATATATTTGA
2533419 TACCCATATATTTGA
1 TACCCATATATTTGA
2533434 T
1 T
2533435 TTTCCATAAA
Statistics
Matches: 64, Mismatches: 21, Indels: 11
0.67 0.22 0.11
Matches are distributed among these distances:
14 11 0.17
15 42 0.66
16 11 0.17
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (15 bp):
TACCCATATATTTGA
Found at i:2537949 original size:30 final size:30
Alignment explanation
Indices: 2537913--2537994 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
2537903 AATATCTCGG
2537913 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
2537943 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
2537973 TACCCATATATTTGATTTTCCA
1 TACCCATATCTTTGACTTTCCA
2537995 TAAATATGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTGA
Found at i:2537956 original size:15 final size:15
Alignment explanation
Indices: 2537913--2537988 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
2537903 AATATCTCGG
*
2537913 TACCCATATCTTTGA
1 TACCCATATATTTGA
**
2537928 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
*
2537943 TACCCATATCTTTGA
1 TACCCATATATTTGA
** *
2537958 CTTTCTAT-TATTTGA
1 -TACCCATATATTTGA
2537973 TACCCATATATTTGA
1 TACCCATATATTTGA
2537988 T
1 T
2537989 TTTCCATAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
14 8 0.18
15 28 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (15 bp):
TACCCATATATTTGA
Found at i:2544297 original size:29 final size:29
Alignment explanation
Indices: 2544261--2544327 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
2544251 CACTTGGAAC
2544261 ATGTAAGAAATCCATTTGCATTAAACAAA
1 ATGTAAGAAATCCATTTGCATTAAACAAA
* *
2544290 ATGTAAGAAATCTATTTGTATTAAACAAA
1 ATGTAAGAAATCCATTTGCATTAAACAAA
2544319 ATGTAAGAA
1 ATGTAAGAA
2544328 TGCATGTGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (29 bp):
ATGTAAGAAATCCATTTGCATTAAACAAA
Found at i:2551274 original size:14 final size:14
Alignment explanation
Indices: 2551250--2551314 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
2551240 AAATTGAATC
2551250 AAATCAAAATTTCAT
1 AAAT-AAAATTTCAT
* *
2551265 ATATAAAATTACAT
1 AAATAAAATTTCAT
2551279 AAAATTAAAATTT-ATT
1 -AAA-TAAAATTTCA-T
*
2551295 AAATAAAAATTCAT
1 AAATAAAATTTCAT
*
2551309 ATATAA
1 AAATAA
2551315 TTTTGATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 22 0.55
15 10 0.25
16 8 0.20
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATAAAATTTCAT
Found at i:2552091 original size:81 final size:80
Alignment explanation
Indices: 2551933--2552098 Score: 287
Period size: 81 Copynumber: 2.1 Consensus size: 80
2551923 TTCTACTATT
* * * *
2551933 AGAAAAATATAAGAATGACGTGAAATCACAGTTTCATACAATTTTTCTCTTAGTAACTTGAGTTT
1 AGAAAAAGATAAAAATGACGTAAAATCACAGCTTCATACAATTTTTCTCTTAGTAACTTGAGTTT
2551998 CTAAATAACCAACCG
66 CTAAATAACCAACCG
2552013 AGAAAAAGATAAAAATGACGTAAAATCACAGCTTCATACAATTCTTTCTCTTAGTAACTTGAGTT
1 AGAAAAAGATAAAAATGACGTAAAATCACAGCTTCATACAATT-TTTCTCTTAGTAACTTGAGTT
2552078 TCTAAATAACCAACCG
65 TCTAAATAACCAACCG
2552094 AGAAA
1 AGAAA
2552099 TCAGGAACAG
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 39 0.48
81 42 0.52
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (80 bp):
AGAAAAAGATAAAAATGACGTAAAATCACAGCTTCATACAATTTTTCTCTTAGTAACTTGAGTTT
CTAAATAACCAACCG
Found at i:2555417 original size:22 final size:21
Alignment explanation
Indices: 2555377--2555417 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2555367 GGTAAAGTAT
**
2555377 ATCAAATTTATTTTGAAATTG
1 ATCAAATTTATTTAAAAATTG
2555398 ATCAACATTTATTTAAAAAT
1 ATCAA-ATTTATTTAAAAAT
2555418 AATTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (21 bp):
ATCAAATTTATTTAAAAATTG
Done.