Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 73
Found at i:6236233 original size:5 final size:5
Alignment explanation
Indices: 6236225--6236249 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6236215 GATAAGATAA
6236225 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
6236250 TTAAACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:6238693 original size:24 final size:24
Alignment explanation
Indices: 6238661--6238710 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
6238651 CTATGATTTG
6238661 GACAAAAAGGAAAGTTAAGTATGA
1 GACAAAAAGGAAAGTTAAGTATGA
6238685 GACAAAAAGGAAAGTTAAGTATGA
1 GACAAAAAGGAAAGTTAAGTATGA
6238709 GA
1 GA
6238711 TTTATTGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.26, T:0.16
Consensus pattern (24 bp):
GACAAAAAGGAAAGTTAAGTATGA
Found at i:6239826 original size:517 final size:518
Alignment explanation
Indices: 6238852--6239885 Score: 1908
Period size: 517 Copynumber: 2.0 Consensus size: 518
6238842 ACATGTTGTT
*
6238852 TTCCAAATGAATTTGAGATTCAACCAAATTTGATTGATGAAAGAACCGGTTAAGATACTAGAACA
1 TTCCAAATGAATTTGAGATTCAACCAAATTTGAATGATGAAAGAACCGGTTAAGATACTAGAACA
6238917 CGGAGCTAAAGGACTAAGGAATTAAACCATTCCATCTATTATGTTAAAGTTATTTGGAGGAATTT
66 CGGAGCTAAAGGACTAAGGAATTAAACCATTCCATCTATTATGTTAAAGTTATTTGGAGGAATTT
*
6238982 TGAAGTCAGGGAAATTATGTGGATAAGTAAATGAGATATGAAAAAAGTAGTATTCTCATGCTTTT
131 TGAAGTCAGGGAAATTATGTGGATAAGCAAATGAGATATGAAAAAAGTAGTATTCTCATGCTTTT
6239047 GCATCAGGTACGTGTTGAAAATAAAAGGACAAATTTTCTTAAGGAGGGAGAATTGTAATATCCCA
196 GCATCAGGTACGTGTTGAAAATAAAAGGACAAATTTTCTTAAGGAGGGAGAATTGTAATATCCCA
* * *
6239112 AATTTTGGGCTAGTGACTAGAATGTAAAATTTGAAAGTTTGGAGACTAATGTGTAAAGTTGTAAA
261 AATTTTGGGCTAGTGACTAGAATATAAAATTTAAAAGTTTGGAGACTAAAGTGTAAAGTTGTAAA
*
6239177 ACTTTAAGGACTAAAAATATAATTTTTCAAAAGTTATATTTTGGATTTGTAAATTAATATTTTAA
326 ACTTTAAGGACTAAAAATATAAATTTTCAAAAGTTATATTTTGGATTTGTAAATTAATATTTTAA
*
6239242 ATCAAGATAATTAGTATAGTGGGTTTTAGAATTTTGATCTGGAGTTTGTATAAAAGTTTATTAAA
391 ATCAAGATAATTAGTATAGTGGGTTTTAGAATTTTGATATGGAGTTTGTATAAAAGTTTATTAAA
**
6239307 GGACAAAGATTGGTCTATTATTTAAATAACCGGATCGAATCAAAAGATTACAAAACTTTCAAG
456 GGACAAAGACCGGTCTATTATTTAAATAACCGGATCGAATCAAAAGATTACAAAACTTTCAAG
*
6239370 TTCCAAATGAATTTGAGATTCAACCAGATTTGAATGATGAAAGAACCGGTTAAGATACTAGAACA
1 TTCCAAATGAATTTGAGATTCAACCAAATTTGAATGATGAAAGAACCGGTTAAGATACTAGAACA
*
6239435 CGGAGCTAAAGGACTAAGGAATTAAACTATTCCATCTATTATGTTAAAGTTATTTGGAGGAATTT
66 CGGAGCTAAAGGACTAAGGAATTAAACCATTCCATCTATTATGTTAAAGTTATTTGGAGGAATTT
6239500 TGAAGTCAGGGAAATTATGTGGATAAGCAAATGAGATATG-AAAAAGTAGTATTCTCATGCTTTT
131 TGAAGTCAGGGAAATTATGTGGATAAGCAAATGAGATATGAAAAAAGTAGTATTCTCATGCTTTT
6239564 GCATCAGGTACGTGTTGAAAATAAAAGGACAAATTTTCTTAAGGAGGGAGAATTGTAATATCCCA
196 GCATCAGGTACGTGTTGAAAATAAAAGGACAAATTTTCTTAAGGAGGGAGAATTGTAATATCCCA
* *
6239629 AATTTTGGGCTGGTGAGTAGAATATAAAATTTAAAAGTTTGGAGACTAAAGTGTAAAGTTGTAAA
261 AATTTTGGGCTAGTGACTAGAATATAAAATTTAAAAGTTTGGAGACTAAAGTGTAAAGTTGTAAA
*
6239694 ACTTTAAGGACTAAAAATATAAATTTTCAAAAGTTATATTTTGGATTTGTAAATTAGTATTTTAA
326 ACTTTAAGGACTAAAAATATAAATTTTCAAAAGTTATATTTTGGATTTGTAAATTAATATTTTAA
*
6239759 ATCATGATAATTAGTATAGTGGGTTTTAGAATTTTGATATGGAGTTTGTATAAAAGTTTATTAAA
391 ATCAAGATAATTAGTATAGTGGGTTTTAGAATTTTGATATGGAGTTTGTATAAAAGTTTATTAAA
* *
6239824 GGACAAAGACCGTTCTATTATTTGAATAACCGGATCGAATCAAAAGATTACAAAACTTTCAA
456 GGACAAAGACCGGTCTATTATTTAAATAACCGGATCGAATCAAAAGATTACAAAACTTTCAA
6239886 AAAAATGTAT
Statistics
Matches: 499, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
517 333 0.67
518 166 0.33
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (518 bp):
TTCCAAATGAATTTGAGATTCAACCAAATTTGAATGATGAAAGAACCGGTTAAGATACTAGAACA
CGGAGCTAAAGGACTAAGGAATTAAACCATTCCATCTATTATGTTAAAGTTATTTGGAGGAATTT
TGAAGTCAGGGAAATTATGTGGATAAGCAAATGAGATATGAAAAAAGTAGTATTCTCATGCTTTT
GCATCAGGTACGTGTTGAAAATAAAAGGACAAATTTTCTTAAGGAGGGAGAATTGTAATATCCCA
AATTTTGGGCTAGTGACTAGAATATAAAATTTAAAAGTTTGGAGACTAAAGTGTAAAGTTGTAAA
ACTTTAAGGACTAAAAATATAAATTTTCAAAAGTTATATTTTGGATTTGTAAATTAATATTTTAA
ATCAAGATAATTAGTATAGTGGGTTTTAGAATTTTGATATGGAGTTTGTATAAAAGTTTATTAAA
GGACAAAGACCGGTCTATTATTTAAATAACCGGATCGAATCAAAAGATTACAAAACTTTCAAG
Found at i:6240900 original size:21 final size:21
Alignment explanation
Indices: 6240858--6240906 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
6240848 AATTTAAAAG
6240858 ATTTAGATGCAAGCTTTGGAAA
1 ATTTAGATGCAAGC-TTGGAAA
6240880 ATTTAGATGCAATGC-TGGAAA
1 ATTTAGATGCAA-GCTTGGAAA
*
6240901 TTTTAG
1 ATTTAG
6240907 TTAAAATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 11 0.44
22 12 0.48
23 2 0.08
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (21 bp):
ATTTAGATGCAAGCTTGGAAA
Found at i:6242697 original size:26 final size:26
Alignment explanation
Indices: 6242637--6242697 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
6242627 GAGCAAGGAA
6242637 AAGGTTTGAAATGGAATGAAAAGTAC
1 AAGGTTTGAAATGGAATGAAAAGTAC
** *
6242663 AAGAATTGAAGT-GAGATGGAAAAGTAC
1 AAGGTTTGAAATGGA-AT-GAAAAGTAC
6242690 -AGGTTTGA
1 AAGGTTTGA
6242698 TCTACTTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 2 0.07
26 17 0.61
27 9 0.32
ACGTcount: A:0.44, C:0.03, G:0.30, T:0.23
Consensus pattern (26 bp):
AAGGTTTGAAATGGAATGAAAAGTAC
Found at i:6245735 original size:22 final size:22
Alignment explanation
Indices: 6245704--6245778 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
6245694 CTTTGTTTTA
6245704 TTTTAATTTGATAGTTTTGCAT
1 TTTTAATTTGATAGTTTTGCAT
* * *
6245726 TTTTATTTTGTCTTTGTTTT--A-
1 TTTTAATTTG--ATAGTTTTGCAT
6245747 TTTTAATTTGATAGTTTTGCAT
1 TTTTAATTTGATAGTTTTGCAT
* *
6245769 ATTTATTTTG
1 TTTTAATTTG
6245779 TCTTGACCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 6 0.15
21 10 0.25
22 18 0.45
24 6 0.15
ACGTcount: A:0.19, C:0.04, G:0.12, T:0.65
Consensus pattern (22 bp):
TTTTAATTTGATAGTTTTGCAT
Found at i:6245737 original size:43 final size:43
Alignment explanation
Indices: 6245689--6245782 Score: 179
Period size: 43 Copynumber: 2.2 Consensus size: 43
6245679 TGAATCAAAG
*
6245689 TTTGTCTTTGTTTTATTTTAATTTGATAGTTTTGCATTTTTAT
1 TTTGTCTTTGTTTTATTTTAATTTGATAGTTTTGCATATTTAT
6245732 TTTGTCTTTGTTTTATTTTAATTTGATAGTTTTGCATATTTAT
1 TTTGTCTTTGTTTTATTTTAATTTGATAGTTTTGCATATTTAT
6245775 TTTGTCTT
1 TTTGTCTT
6245783 GACCAAACTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.16, C:0.05, G:0.12, T:0.67
Consensus pattern (43 bp):
TTTGTCTTTGTTTTATTTTAATTTGATAGTTTTGCATATTTAT
Found at i:6245776 original size:21 final size:21
Alignment explanation
Indices: 6245709--6245776 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
6245699 TTTTATTTTA
*
6245709 ATTTGATAGTTTTGCATTTTT
1 ATTTGATAGTTTTGCATATTT
**
6245730 ATTT--T-GTCTTTGTTTTATTTT
1 ATTTGATAGT-TTTG-CATA-TTT
6245751 AATTTGATAGTTTTGCATATTT
1 -ATTTGATAGTTTTGCATATTT
6245773 ATTT
1 ATTT
6245777 TGTCTTGACC
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 1 0.03
21 11 0.31
22 7 0.20
23 2 0.06
24 5 0.14
25 2 0.06
ACGTcount: A:0.19, C:0.04, G:0.12, T:0.65
Consensus pattern (21 bp):
ATTTGATAGTTTTGCATATTT
Found at i:6247101 original size:20 final size:20
Alignment explanation
Indices: 6247076--6247113 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6247066 ACTATGACCC
6247076 AAAGTATCGATACTCTTGAA
1 AAAGTATCGATACTCTTGAA
*
6247096 AAAGTATGGATACTCTTG
1 AAAGTATCGATACTCTTG
6247114 CTAAGAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (20 bp):
AAAGTATCGATACTCTTGAA
Found at i:6250309 original size:45 final size:45
Alignment explanation
Indices: 6250227--6250328 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 45
6250217 AAGATTAGAT
*
6250227 TTATTATTTTATTAGGAATTAAGATCGAGTTAAAACATTATTCTTAGTTTA
1 TTATTA-TTTATTAGGAATTAAGA-C-AGTTAAAACA-T-GT-TTAGTTTA
*
6250278 TTATTATTTATTAGGAATT-AGA-A-TTAGAACATGTTTAGTTTA
1 TTATTATTTATTAGGAATTAAGACAGTTAAAACATGTTTAGTTTA
6250320 TTATTATTT
1 TTATTATTT
6250329 TATTTATTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
42 17 0.35
43 1 0.02
44 1 0.02
45 7 0.14
46 1 0.02
49 3 0.06
50 13 0.27
51 6 0.12
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (45 bp):
TTATTATTTATTAGGAATTAAGACAGTTAAAACATGTTTAGTTTA
Found at i:6260232 original size:116 final size:116
Alignment explanation
Indices: 6259982--6260404 Score: 275
Period size: 116 Copynumber: 3.6 Consensus size: 116
6259972 CAAAAATGAT
* * * *
6259982 GAAGCTATCAAAGGAAGAAGAAGTTCATGTACGAGTGTTTGTTCAACCTCGATATGGCCTTTGTG
1 GAAGCTATCAAA-GAAGAAGAAGTTCATATACGAGTGCTTATTCAACCTCAATATGGCCTTTGTG
* * * *
6260047 GGAGAGTAGCAAATTTATATAGGAAAGCTCGTATAGTTTGTTCATAAAGGAT
65 GGAGAGTAACAAATTTATATAGGAAAGCTCGTATAGTTTATTCAGAAAGGAG
* * * * *
6260099 AAAACTAT-ATCAA-AAGAAGACGTTCATATATGA-TAGCTTATTTAACCTCAATATGGCCTTTG
1 GAAGCTATCA--AAGAAGAAGAAGTTCATATACGAGT-GCTTATTCAACCTCAATATGGCCTTTG
* * *
6260161 -GGAGAGAGTAAC-AGTTTATATA-GAAGATCTCGTCTAGTTTATTCAGAAAGGAG
63 TGG-GAGAGTAACAAATTTATATAGGAA-AGCTCGTATAGTTTATTCAGAAAGGAG
* * * * ** * * * * *
6260214 GAAGCTATCAAATGAAGAAGGATTTCATTTATGAGAACTTTTTCGATCTCAATATGGCATTTTTG
1 GAAGCTATCAAA-GAAGAAGAAGTTCATATACGAGTGCTTATTCAACCTCAATATGGCCTTTGTG
*** * * * * * * * *
6260279 GGAGAGTAGGGAGTTCATATAGGATATCTCATCTAGTTTGTTCAAAAAGAGAG
65 GGAGAGTAACAAATTTATATAGGAAAGCTCGTATAGTTTATTCAGAAAG-GAG
** ** * * * * * *
6260332 GAAATTATCAAAAGATTAA-ATAGTTCATATAGGAGAGTTTATTCGACCTTAATATAGCCTTTGT
1 GAAGCTATC-AAAGAAGAAGA-AGTTCATATACGAGTGCTTATTCAACCTCAATATGGCCTTTGT
6260396 GGGAGAGTA
64 GGGAGAGTA
6260405 TAGAGTTCAT
Statistics
Matches: 238, Mismatches: 53, Indels: 29
0.74 0.17 0.09
Matches are distributed among these distances:
114 5 0.02
115 40 0.17
116 93 0.39
117 38 0.16
118 59 0.25
119 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (116 bp):
GAAGCTATCAAAGAAGAAGAAGTTCATATACGAGTGCTTATTCAACCTCAATATGGCCTTTGTGG
GAGAGTAACAAATTTATATAGGAAAGCTCGTATAGTTTATTCAGAAAGGAG
Found at i:6269213 original size:10 final size:10
Alignment explanation
Indices: 6269193--6269234 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
6269183 TAACGAGCTA
6269193 TGAGAGAATT
1 TGAGAGAATT
* *
6269203 TAAGAGTATT
1 TGAGAGAATT
6269213 TGAGAGAATT
1 TGAGAGAATT
*
6269223 TGAGAGGATT
1 TGAGAGAATT
6269233 TG
1 TG
6269235 GTGTGATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (10 bp):
TGAGAGAATT
Found at i:6269216 original size:20 final size:20
Alignment explanation
Indices: 6269193--6269234 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6269183 TAACGAGCTA
*
6269193 TGAGAGAATTTAAGAGTATT
1 TGAGAGAATTTAAGAGGATT
*
6269213 TGAGAGAATTTGAGAGGATT
1 TGAGAGAATTTAAGAGGATT
6269233 TG
1 TG
6269235 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (20 bp):
TGAGAGAATTTAAGAGGATT
Found at i:6271473 original size:25 final size:26
Alignment explanation
Indices: 6271435--6271503 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
6271425 CATGTTTTGG
6271435 AAAAAATGAT-TTTTAAAAGTG-TTAT
1 AAAAAAT-ATATTTTAAAAGTGATTAT
* *
6271460 AGAAAATATATTTTAAAAGTGATTTT
1 AAAAAATATATTTTAAAAGTGATTAT
* *
6271486 AAAAAATACAATTTAAAA
1 AAAAAATATATTTTAAAA
6271504 TTTAACTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.05
25 17 0.46
26 18 0.49
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (26 bp):
AAAAAATATATTTTAAAAGTGATTAT
Found at i:6272211 original size:16 final size:16
Alignment explanation
Indices: 6272190--6272247 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
6272180 ACAGAGCCTC
*
6272190 TGAATCATTCAGCATT
1 TGAATCATTCAACATT
6272206 TGAATCATTCAACATT
1 TGAATCATTCAACATT
**
6272222 TGAATCATTCAACGCT
1 TGAATCATTCAACATT
6272238 T-AATCATTCA
1 TGAATCATTCA
6272248 GCGCTTAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 9 0.23
16 30 0.77
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:6272244 original size:15 final size:15
Alignment explanation
Indices: 6272208--6272261 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
6272198 TCAGCATTTG
**
6272208 AATCATTCAACATTT
1 AATCATTCAACGCTT
6272223 GAATCATTCAACGCTT
1 -AATCATTCAACGCTT
*
6272239 AATCATTCAGCGCTT
1 AATCATTCAACGCTT
6272254 AATCATTC
1 AATCATTC
6272262 TGAAGTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
15 22 0.63
16 13 0.37
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.35
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:6273654 original size:81 final size:81
Alignment explanation
Indices: 6273519--6274093 Score: 814
Period size: 81 Copynumber: 7.1 Consensus size: 81
6273509 TTCCTTTAGA
* * * * * * ** *
6273519 CTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATAATTGACACTTTTCTATCAAGTGCA
1 CTTTTACTCAAAGGTAATTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
* *
6273584 CAGCTAGACCATTAAT
66 CAGCTAGGCTATTAAT
* *
6273600 CTTTTACTCAAAGGTAATTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTAATTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
6273665 CAGCTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* * * *
6273681 CTTTAATTCAAAGGT-ATCTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGCCAAATAC
1 CTTTTACTCAAAGGTAAT-TAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
6273745 ACAGCTAGGCTATTAAT
65 ACAGCTAGGCTATTAAT
* * *
6273762 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGTATAATTGACACCTTTCTGCCAAATGCA
1 CTTTTACTCAAAGGTAATTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
* *
6273827 CAACTAGGTTATTAAT
66 CAGCTAGGCTATTAAT
* *
6273843 CTTTTACTCAAAGGT-ATCTAAACTTTCATCTAACTGGCATAAATGACACCTTTCTGCCAAATGC
1 CTTTTACTCAAAGGTAAT-TAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
6273907 ACAGCTAGGCTATTAAT
65 ACAGCTAGGCTATTAAT
* * *
6273924 CATTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCA
1 CTTTTACTCAAAGGTAATTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
*
6273989 CAGCTAGGCCATTAAT
66 CAGCTAGGCTATTAAT
* * *
6274005 CTTTTACCCAAAGGT-ATCTATCCTTTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGC
1 CTTTTACTCAAAGGTAAT-TAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
6274069 ACAGGTAGGCTATTAAT
65 ACAGCTAGGCTATTAAT
6274086 CTTTTACT
1 CTTTTACT
6274094 TTAAAATAGT
Statistics
Matches: 442, Mismatches: 47, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
80 4 0.01
81 436 0.99
82 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (81 bp):
CTTTTACTCAAAGGTAATTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA
CAGCTAGGCTATTAAT
Found at i:6275035 original size:3 final size:3
Alignment explanation
Indices: 6275020--6275075 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
6275010 GTAATATCAT
* * **
6275020 TAA TAA AAA TAA TAA TAA TAA TAAA TAA TTA TGTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA
6275067 TAA TAA TAA
1 TAA TAA TAA
6275076 ATATACTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 40 0.89
4 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:6281941 original size:34 final size:33
Alignment explanation
Indices: 6281898--6281981 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 33
6281888 TCTCGCCTCG
6281898 ATTATATATATAATATTTTATATATTTTATATTA
1 ATTATATATATAATATTTTATAT-TTTTATATTA
*
6281932 ATTATATATATAATATTTTTTATTTTTATATTA
1 ATTATATATATAATATTTTATATTTTTATATTA
*
6281965 AATATATATATATATAT
1 ATTATATATATA-ATAT
6281982 ATATAATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 21 0.45
34 26 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
ATTATATATATAATATTTTATATTTTTATATTA
Found at i:6283627 original size:27 final size:26
Alignment explanation
Indices: 6283597--6283659 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
6283587 ATAATGAAAA
* *
6283597 ATATAATA-AATTATGTTTATATGAACT
1 ATATAATATAATTA--TCTATATAAACT
6283624 ATAT-ATATAATTATCTATATAAACT
1 ATATAATATAATTATCTATATAAACT
6283649 ATATATATATA
1 ATATA-ATATA
6283660 TATAAACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 14 0.45
26 3 0.10
27 14 0.45
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (26 bp):
ATATAATATAATTATCTATATAAACT
Found at i:6283661 original size:19 final size:20
Alignment explanation
Indices: 6283639--6283748 Score: 67
Period size: 19 Copynumber: 5.7 Consensus size: 20
6283629 TATAATTATC
6283639 TATATAAACTATA-TATATA
1 TATATAAACTATAGTATATA
6283658 TATATAAACTATAAAAAAGTATATA
1 TATATAAACTAT-----AGTATATA
*
6283683 GTTTATAAACTATA--AT-T-
1 -TATATAAACTATAGTATATA
*
6283700 TATATTAA-TATAGTATATA
1 TATATAAACTATAGTATATA
*
6283719 TATATAAA--A-ACTATATA
1 TATATAAACTATAGTATATA
*
6283736 TGTATAAACTATA
1 TATATAAACTATA
6283749 TAAAATATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 27
0.68 0.06 0.26
Matches are distributed among these distances:
15 4 0.06
16 6 0.08
17 16 0.23
18 3 0.04
19 22 0.31
20 1 0.01
21 1 0.01
24 1 0.01
25 6 0.08
26 11 0.15
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (20 bp):
TATATAAACTATAGTATATA
Found at i:6283697 original size:52 final size:52
Alignment explanation
Indices: 6283641--6283748 Score: 123
Period size: 52 Copynumber: 2.1 Consensus size: 52
6283631 TAATTATCTA
* *
6283641 TATAAACTATA-TATATATA-TATAAACTATA-AAAAAGTATATAGTTTATAAAC
1 TATAAACTATATTA-ATATAGTATAAA-TATATAAAAACTATATA-TGTATAAAC
** *
6283693 TATAATTTATATTAATATAGTATATATATATAAAAACTATATATGTATAAAC
1 TATAAACTATATTAATATAGTATAAATATATAAAAACTATATATGTATAAAC
6283745 TATA
1 TATA
6283749 TAAAATATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
52 30 0.62
53 18 0.38
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (52 bp):
TATAAACTATATTAATATAGTATAAATATATAAAAACTATATATGTATAAAC
Found at i:6283819 original size:77 final size:78
Alignment explanation
Indices: 6283652--6283800 Score: 255
Period size: 77 Copynumber: 1.9 Consensus size: 78
6283642 ATAAACTATA
*
6283652 TATATATATATAAACTATAAAAAAGTATATAGTTTATAAACTATAATTTATATTAATATAGTATA
1 TATATATATATAAACTATAAAAAAGTATATAGTTTATAAACTACAATTTATATTAATATAGTATA
6283717 TATATATAAAAAC
66 TATATATAAAAAC
* * *
6283730 TATATATGTATAAACTATATAAAA-TATATAGTTTATAAATTACAATTTATATTAATATAGTATA
1 TATATATATATAAACTATAAAAAAGTATATAGTTTATAAACTACAATTTATATTAATATAGTATA
6283794 TATATAT
66 TATATAT
6283801 GTATGTATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 45 0.67
78 22 0.33
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (78 bp):
TATATATATATAAACTATAAAAAAGTATATAGTTTATAAACTACAATTTATATTAATATAGTATA
TATATATAAAAAC
Found at i:6284048 original size:16 final size:16
Alignment explanation
Indices: 6284027--6284057 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6284017 TAATTCGTAT
6284027 ATAGTTTATATAAATA
1 ATAGTTTATATAAATA
6284043 ATAGTTTATATAAAT
1 ATAGTTTATATAAAT
6284058 TATATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATAGTTTATATAAATA
Found at i:6284132 original size:11 final size:11
Alignment explanation
Indices: 6284118--6284235 Score: 66
Period size: 11 Copynumber: 10.5 Consensus size: 11
6284108 ACCTATAGTG
6284118 TATATAAACTA
1 TATATAAACTA
6284129 TATATATAACCTA
1 TATATA-AA-CTA
**
6284142 TCATAT-ATGTA
1 T-ATATAAACTA
*
6284153 TGTATACAATCTA
1 TATATA-AA-CTA
6284166 TAGTATAAACTA
1 TA-TATAAACTA
* *
6284178 TGTAT--AGTA
1 TATATAAACTA
6284187 TATATAAACTA
1 TATATAAACTA
* *
6284198 TGTAT--AGTA
1 TATATAAACTA
6284207 TATATAAACTA
1 TATATAAACTA
*
6284218 TATATAACCTA
1 TATATAAACTA
6284229 TAGTATA
1 TA-TATA
6284236 TGTATGTATA
Statistics
Matches: 80, Mismatches: 15, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
9 14 0.17
10 3 0.04
11 34 0.43
12 12 0.15
13 9 0.11
14 8 0.10
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (11 bp):
TATATAAACTA
Found at i:6284194 original size:20 final size:20
Alignment explanation
Indices: 6284164--6284223 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
6284154 GTATACAATC
6284164 TATAGTATAAACTATGTATAG
1 TATA-TATAAACTATGTATAG
6284185 TATATATAAACTATGTATAG
1 TATATATAAACTATGTATAG
*
6284205 TATATATAAACTATATATA
1 TATATATAAACTATGTATA
6284224 ACCTATAGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 34 0.89
21 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (20 bp):
TATATATAAACTATGTATAG
Found at i:6284210 original size:87 final size:87
Alignment explanation
Indices: 6284111--6284279 Score: 252
Period size: 87 Copynumber: 1.9 Consensus size: 87
6284101 ATATGTAACC
*
6284111 TATAGTGTATATAAACTATATATATAACCTATCA-TATATGTATGTATACAATCTATAGTATA-A
1 TATAGTATATATAAAC--TATATATAACCTAT-AGTATATGTATGTATACAATCTATAGTATATA
6284174 ACTATGTATAGTATATATAAACTATG
63 ACTATGTATA-TATATATAAACTATG
* **
6284200 TATAGTATATATAAACTATATATAACCTATAGTATATGTATGTATACAATCTATAGTGTATATGT
1 TATAGTATATATAAACTATATATAACCTATAGTATATGTATGTATACAATCTATAGTATATAACT
6284265 ATGTATATATATATA
66 ATGTATATATATATA
6284280 TATATATAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
86 1 0.01
87 49 0.66
88 9 0.12
89 15 0.20
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (87 bp):
TATAGTATATATAAACTATATATAACCTATAGTATATGTATGTATACAATCTATAGTATATAACT
ATGTATATATATATAAACTATG
Found at i:6284230 original size:20 final size:20
Alignment explanation
Indices: 6284169--6284230 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
6284159 CAATCTATAG
* **
6284169 TATAAACTATGTATAGTATA
1 TATAAACTATATATAACATA
* **
6284189 TATAAACTATGTATAGTATA
1 TATAAACTATATATAACATA
*
6284209 TATAAACTATATATAACCTA
1 TATAAACTATATATAACATA
6284229 TA
1 TA
6284231 GTATATGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (20 bp):
TATAAACTATATATAACATA
Found at i:6284554 original size:62 final size:62
Alignment explanation
Indices: 6284452--6284582 Score: 217
Period size: 62 Copynumber: 2.1 Consensus size: 62
6284442 TTATTAAAAA
*
6284452 AATAGTTGTTGTAAATATATATTATATTATAATCATTTAATACAACAGAACAATCAGTAACT
1 AATAATTGTTGTAAATATATATTATATTATAATCATTTAATACAACAGAACAATCAGTAACT
* * * *
6284514 AATAATTGTTGTAAATATATATTATATTATAATCATTTAATACAATAGAATAATTAGTGACT
1 AATAATTGTTGTAAATATATATTATATTATAATCATTTAATACAACAGAACAATCAGTAACT
6284576 AATAATT
1 AATAATT
6284583 TACAGGTTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.40
Consensus pattern (62 bp):
AATAATTGTTGTAAATATATATTATATTATAATCATTTAATACAACAGAACAATCAGTAACT
Found at i:6284610 original size:16 final size:16
Alignment explanation
Indices: 6284584--6284622 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6284574 CTAATAATTT
*
6284584 ACAGGTTAGGTT-AAA
1 ACAGGTCAGGTTGAAA
6284599 ATCAGGTCAGGTTGAAA
1 A-CAGGTCAGGTTGAAA
6284616 ACAGGTC
1 ACAGGTC
6284623 GGGTAATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:6285249 original size:21 final size:20
Alignment explanation
Indices: 6285215--6285253 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6285205 ATTAATTATT
6285215 TAAAAAATTAAATAAAAATA
1 TAAAAAATTAAATAAAAATA
*
6285235 TAAAAACATTTAATAAAAA
1 TAAAAA-ATTAAATAAAAA
6285254 CAGTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAAATTAAATAAAAATA
Found at i:6286810 original size:19 final size:19
Alignment explanation
Indices: 6286761--6286831 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
6286751 ATAATGAGGA
6286761 AAAATACAAAGAAAATAGAAA-
1 AAAATA-AAA-AAAATA-AAAT
*
6286782 AAAATGAAAAAAAATACAAT
1 AAAAT-AAAAAAAATAAAAT
* * *
6286802 TACATAAAATAAATAAAAT
1 AAAATAAAAAAAATAAAAT
6286821 AAAATAAAAAA
1 AAAATAAAAAA
6286832 TTTAAGTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 22 0.55
20 9 0.22
21 8 0.20
22 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (19 bp):
AAAATAAAAAAAATAAAAT
Found at i:6286820 original size:5 final size:5
Alignment explanation
Indices: 6286761--6286829 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
6286751 ATAATGAGGA
* * * *
6286761 AAAAT ACAAAG AAAAT AGAAA- AAAAT GAAAA- AAAAT ACAAT TACAT
1 AAAAT A-AAAT AAAAT A-AAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
6286807 AAAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA
6286830 AATTTAAGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
4 11 0.22
5 28 0.56
6 11 0.22
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:6287001 original size:24 final size:24
Alignment explanation
Indices: 6286974--6287021 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6286964 TATAAACAAG
* *
6286974 GTATAAAAATAATAGTAATAATAA
1 GTATAAAAATAAAAATAATAATAA
*
6286998 GTATTAAAATAAAAATAATAATAA
1 GTATAAAAATAAAAATAATAATAA
6287022 TAGTAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (24 bp):
GTATAAAAATAAAAATAATAATAA
Found at i:6287036 original size:30 final size:30
Alignment explanation
Indices: 6286976--6287036 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
6286966 TAAACAAGGT
* *
6286976 ATAAAAATAATAGTAATAATAAGTATTAAA
1 ATAAAAATAATAATAATAATAAGTAATAAA
*
6287006 ATAAAAATAATAATAATAGTAA-TGAATAAA
1 ATAAAAATAATAATAATAATAAGT-AATAAA
6287036 A
1 A
6287037 AACAGAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (30 bp):
ATAAAAATAATAATAATAATAAGTAATAAA
Found at i:6288452 original size:106 final size:106
Alignment explanation
Indices: 6288262--6288456 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 106
6288252 TATTGCACCA
* * ** **
6288262 AGTCCAATATCCTCGGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAGT
1 AGTCCAATATCCTCGCTCGTGAAGTTGAAATTGACTCTAAAACTGGGAAATTGTTTGTTGACAAC
6288327 CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTCG
66 CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTCG
* * *
6288368 AGTCTAATATCCTTCGCT-GTGAAGTTGAAATTGACTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 AGTCCAATATCC-TCGCTCGTGAAGTTGAAATTGACTCTAAAACTGGGAAATTGTTTGTTGACAA
* *
6288432 CCAGTCGTCCCTTCGTTGTGAAGTT
65 CCAGTCGCCCCTTCGCTGTGAAGTT
6288457 AAACTTGTGT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 73 0.95
107 4 0.05
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTCGCTCGTGAAGTTGAAATTGACTCTAAAACTGGGAAATTGTTTGTTGACAAC
CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTATGCTGTCTCG
Found at i:6288548 original size:16 final size:16
Alignment explanation
Indices: 6288509--6288549 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
6288499 CCTTTGTCGT
*
6288509 GAAGTTAAAATCCAAG
1 GAAGTTGAAATCCAAG
*
6288525 GAAATTGAAATCCAAG
1 GAAGTTGAAATCCAAG
*
6288541 TAAGTTGAA
1 GAAGTTGAA
6288550 TTGCTCCGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.22
Consensus pattern (16 bp):
GAAGTTGAAATCCAAG
Found at i:6302646 original size:20 final size:20
Alignment explanation
Indices: 6302617--6302654 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6302607 CCCCTTCAAA
*
6302617 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
6302637 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
6302655 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:6309600 original size:22 final size:20
Alignment explanation
Indices: 6309551--6309621 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 20
6309541 CAATGAAAGT
*
6309551 AAATAAATAAAACAAAGAAAA
1 AAATAAAT-AAACAAATAAAA
*
6309572 CATATAAATAACACAAATAAACA
1 -AAATAAATAA-ACAAATAAA-A
*
6309595 AAATAAGATAAA-AAATAAGA
1 AAATAA-ATAAACAAATAAAA
6309615 AAATAAA
1 AAATAAA
6309622 AGAAGTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 1 0.02
20 7 0.17
21 8 0.19
22 21 0.50
23 5 0.12
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (20 bp):
AAATAAATAAACAAATAAAA
Found at i:6309881 original size:2 final size:2
Alignment explanation
Indices: 6309874--6309906 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6309864 AGTTATATGA
6309874 AT AT 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 AT AT A
6309907 ATAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6309912 original size:3 final size:3
Alignment explanation
Indices: 6309904--6309992 Score: 51
Period size: 3 Copynumber: 29.3 Consensus size: 3
6309894 ATATATATAT
* * *
6309904 ATA ATA ATA ATA ATA ACTT ATA A-A CA-A AGT- ATA AAA ATA ATA GTA
1 ATA ATA ATA ATA ATA A-TA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA
* * *
6309949 ATA ATA AGTA TTA A-A ATA AAA ATA ATA ATA ATA GTA ATGA ATA A
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA A
6309993 AAAACAGAGA
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
2 5 0.08
3 54 0.82
4 7 0.11
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:6309957 original size:24 final size:24
Alignment explanation
Indices: 6309930--6309979 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
6309920 CTTATAAACA
* *
6309930 AAGTATAAAAATAATAGTAATAAT
1 AAGTATAAAAATAAAAATAATAAT
*
6309954 AAGTATTAAAATAAAAATAATAAT
1 AAGTATAAAAATAAAAATAATAAT
6309978 AA
1 AA
6309980 TAGTAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (24 bp):
AAGTATAAAAATAAAAATAATAAT
Found at i:6309994 original size:30 final size:30
Alignment explanation
Indices: 6309934--6309994 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
6309924 TAAACAAAGT
* *
6309934 ATAAAAATAATAGTAATAATAAGTATTAAA
1 ATAAAAATAATAATAATAATAAGTAATAAA
*
6309964 ATAAAAATAATAATAATAGTAA-TGAATAAA
1 ATAAAAATAATAATAATAATAAGT-AATAAA
6309994 A
1 A
6309995 AACAGAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (30 bp):
ATAAAAATAATAATAATAATAAGTAATAAA
Found at i:6310071 original size:16 final size:16
Alignment explanation
Indices: 6310021--6310082 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
6310011 ATTATAAAGA
6310021 ATATGAAAATCAAAGTAT
1 ATAT-AAAAT-AAAGTAT
* *
6310039 ATATATATATATA-TAT
1 ATATA-AAATAAAGTAT
6310055 ATATAAAATAAAGTAT
1 ATATAAAATAAAGTAT
* *
6310071 AAATGAAATAAA
1 ATATAAAATAAA
6310083 AAATAATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 5 0.14
16 21 0.58
17 3 0.08
18 7 0.19
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (16 bp):
ATATAAAATAAAGTAT
Found at i:6310995 original size:57 final size:59
Alignment explanation
Indices: 6310882--6310997 Score: 200
Period size: 57 Copynumber: 2.0 Consensus size: 59
6310872 TTGACAAACT
*
6310882 TCTTTAACTGGGAAGAAAAAGTTTTAACACAGTCTGAAAACAAATGGAGCAACTCCACC
1 TCTTTAACTGGGAAGAAAAAGTTTTAACACAGTCTGAAAACAAATGGAACAACTCCACC
*
6310941 TCTTTAACTGGGAAGAATAAGTTTT-A-ACAGTCTGAAAACAAATGGAACAACTCCACC
1 TCTTTAACTGGGAAGAAAAAGTTTTAACACAGTCTGAAAACAAATGGAACAACTCCACC
6310998 CCAGTACGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
57 30 0.55
58 1 0.02
59 24 0.44
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (59 bp):
TCTTTAACTGGGAAGAAAAAGTTTTAACACAGTCTGAAAACAAATGGAACAACTCCACC
Found at i:6322839 original size:29 final size:29
Alignment explanation
Indices: 6322803--6322862 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
6322793 CATGTTTGAT
*
6322803 AGAAAATTAAAAATGTTTAGAAATGATGG
1 AGAAAATTAAAAACGTTTAGAAATGATGG
6322832 AGAAAATTAAAAACGTTTAGAAATGATGG
1 AGAAAATTAAAAACGTTTAGAAATGATGG
6322861 AG
1 AG
6322863 TTACCATCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.52, C:0.02, G:0.22, T:0.25
Consensus pattern (29 bp):
AGAAAATTAAAAACGTTTAGAAATGATGG
Found at i:6324584 original size:24 final size:23
Alignment explanation
Indices: 6324557--6324612 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 23
6324547 AATTCCCACC
6324557 TAAACACCCTCCTCCTCCCCTATA
1 TAAAC-CCCTCCTCCTCCCCTATA
*
6324581 TAAACCCCATCCTCCTCTCCTATA
1 TAAACCCC-TCCTCCTCCCCTATA
6324605 TAAACCCC
1 TAAACCCC
6324613 CTTAACCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.27, C:0.48, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAACCCCTCCTCCTCCCCTATA
Found at i:6324773 original size:14 final size:14
Alignment explanation
Indices: 6324754--6324783 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6324744 GTTGTTATAT
*
6324754 ATTTTTTATAAATA
1 ATTTTTTAAAAATA
6324768 ATTTTTTAAAAATA
1 ATTTTTTAAAAATA
6324782 AT
1 AT
6324784 GTTATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTTTAAAAATA
Found at i:6324822 original size:15 final size:14
Alignment explanation
Indices: 6324794--6324850 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
6324784 GTTATATTTT
*
6324794 TTTATTAAAATATTA
1 TTTATT-AATTATTA
6324809 TTTATATAATTATTA
1 TTTAT-TAATTATTA
*
6324824 TTTATTTAAAT-TTA
1 TTTA-TTAATTATTA
*
6324838 TTAATTAATTATT
1 TTTATTAATTATT
6324851 TGTGTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 5 0.14
14 8 0.23
15 20 0.57
16 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTAATTATTA
Found at i:6325990 original size:17 final size:17
Alignment explanation
Indices: 6325968--6326003 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
6325958 GTTTGATATA
6325968 ATTAGAA-TATTATATTT
1 ATTAGAACTA-TATATTT
6325985 ATTAGAACTATATATTT
1 ATTAGAACTATATATTT
6326002 AT
1 AT
6326004 ATTTCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTAGAACTATATATTT
Found at i:6326617 original size:42 final size:42
Alignment explanation
Indices: 6326558--6326708 Score: 178
Period size: 42 Copynumber: 3.6 Consensus size: 42
6326548 GATTATGATA
* * *
6326558 CCACAAGGGTACATGCCTAACCCACCAGTTCAGATGCCATCT
1 CCACAAGGGTATATGCCTAGCCCACCAGTTCATATGCCATCT
* *
6326600 CCACAAGGGTATATGCCTAGCCCACCATTTCATATGTCATCT
1 CCACAAGGGTATATGCCTAGCCCACCAGTTCATATGCCATCT
* * *
6326642 CCGCAGGGGTATATGGCC-AGCCTACCAGTTCATATGCCATCT
1 CCACAAGGGTATAT-GCCTAGCCCACCAGTTCATATGCCATCT
* * * *
6326684 CCGCAAGGTTACATTCCTAGCCCAC
1 CCACAAGGGTATATGCCTAGCCCAC
6326709 AGGGGTACAT
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
41 2 0.02
42 87 0.95
43 3 0.03
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (42 bp):
CCACAAGGGTATATGCCTAGCCCACCAGTTCATATGCCATCT
Found at i:6326749 original size:21 final size:21
Alignment explanation
Indices: 6326684--6326749 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
6326674 TATGCCATCT
* *
6326684 CCGCAAGGTTACATTCCTAGC
1 CCGCAAGGTTACATACCCAGC
* * *
6326705 CCACAGGGGTACATACCCAGC
1 CCGCAAGGTTACATACCCAGC
*
6326726 CCGCAAGGTTACATGCCCAGC
1 CCGCAAGGTTACATACCCAGC
6326747 CCG
1 CCG
6326750 TAGAGTTTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
CCGCAAGGTTACATACCCAGC
Found at i:6327507 original size:21 final size:21
Alignment explanation
Indices: 6327481--6327522 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6327471 TTTTTAACTT
6327481 TAAATAATAATTAATATATTC
1 TAAATAATAATTAATATATTC
*
6327502 TAAATAATATTTAATATATTC
1 TAAATAATAATTAATATATTC
6327523 GAATGACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATAATAATTAATATATTC
Found at i:6327817 original size:137 final size:134
Alignment explanation
Indices: 6327614--6327996 Score: 475
Period size: 136 Copynumber: 2.8 Consensus size: 134
6327604 ATAATGAATA
* *
6327614 ATAGGTGATGACGTGAATAGTGCCCCACCGGGGGACATCACATATAAT-AGGACAATTATAACAT
1 ATAGGTGTTGACGTGAATAGTG-CCC-CCGGGGGACATCACACATAATAAGG-CAATTAT-ACAT
* *
6327678 ATTCTCTGACAAAAAGGAAAGGCACATCCCACAAGAAGCACTTTCACCACATTGTTACGTCCCCT
62 ATTCTCTGACAAAAAGGAAAGGCGCATCCCACAAGAAGCGCTTTCACCACATTGTTACGTCCCCT
6327743 CAAACATG
127 CAAACATG
*
6327751 ATAGGTGTTGACGTGAATAGAT-CCTCGCCGGGGGATATCACACATAATAAGGCAATTATAGCAT
1 ATAGGTGTTGACGTGAATAG-TGCC-C-CCGGGGGACATCACACATAATAAGGCAATTATA-CAT
* * * * *
6327815 ATTCTCTGA-AAAAAGGAAAGACGCGTTCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCTT
62 ATTCTCTGACAAAAAGGAAAGGCGCATCCCACAAGAAGCGCTTTCACCACATTGTTACGTCCCCT
6327879 CAAACATG
127 CAAACATG
* * * * * ** * *
6327887 ACATGCGTTTACGTGAATACTGCCCCACAAGGGACATCACACATAATAGGGCAATTATTACCTAT
1 ATAGGTGTTGACGTGAATAGTGCCCC-CGGGGGACATCACACATAATAAGGCAATTA-TACATAT
*
6327952 TTTCTGACAAAAAGGAAAGGCGCATCCCACAAGAAGCGCTTTCAC
64 TCTCTGACAAAAAGGAAAGGCGCATCCCACAAGAAGCGCTTTCAC
6327997 ATGAATAGTG
Statistics
Matches: 213, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
134 1 0.00
135 38 0.18
136 112 0.53
137 58 0.27
138 4 0.02
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (134 bp):
ATAGGTGTTGACGTGAATAGTGCCCCCGGGGGACATCACACATAATAAGGCAATTATACATATTC
TCTGACAAAAAGGAAAGGCGCATCCCACAAGAAGCGCTTTCACCACATTGTTACGTCCCCTCAAA
CATG
Found at i:6333026 original size:135 final size:135
Alignment explanation
Indices: 6332781--6333214 Score: 681
Period size: 135 Copynumber: 3.2 Consensus size: 135
6332771 TAATATGTAA
*
6332781 CGCTTATATAATAAAATAAGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAA
1 CGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAA
*
6332846 AATGTTACCAAGGATAACATAACCGATTAATTACTGGAAACATTATCAACCACAATAACATATTA
66 AATGTTACCAAGGATAACATAACCGATTAATTACTGGAAACATTATCAAGCACAATAACATATTA
6332911 GGTAG
131 GGTAG
* *
6332916 CGTTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATATTAGGTAAACGCCTAA
1 CGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAA
* *
6332981 AATGTTACCAAGGATAACATAATCGATTAATTACTGGAAACATTATCAAGTACAATAACATATTA
66 AATGTTACCAAGGATAACATAACCGATTAATTACTGGAAACATTATCAAGCACAATAACATATTA
6333046 GGTAG
131 GGTAG
* ** * * *
6333051 AGCTTATATAATGTAATAGGTTAATTACTTAATTTGTTATTACAACATATTAAGTAAATGCTTAA
1 CGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAA
* * *
6333116 AATATTACCAAGGATAACATAACCGATTAATTACTGGAAATATTATCAAGCATAATAACATATTA
66 AATGTTACCAAGGATAACATAACCGATTAATTACTGGAAACATTATCAAGCACAATAACATATTA
*
6333181 AGTAG
131 GGTAG
* * * *
6333186 CACTTATGTAACAAAATAGG-TAGTTACTT
1 CGCTTATATAATAAAATAGGTTAATTACTT
6333215 GCTTAATTTG
Statistics
Matches: 272, Mismatches: 27, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
134 8 0.03
135 264 0.97
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (135 bp):
CGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAA
AATGTTACCAAGGATAACATAACCGATTAATTACTGGAAACATTATCAAGCACAATAACATATTA
GGTAG
Found at i:6333521 original size:73 final size:73
Alignment explanation
Indices: 6333276--6333522 Score: 370
Period size: 73 Copynumber: 3.4 Consensus size: 73
6333266 AAAATTTAAA
* * *
6333276 CTACCTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGTTAATAATGCAAATGATAAAAA
1 CTACCTATTACATTAAAATACCTACCAGTTTTTTTGAAGGTTGTTAATAATGTAAACGATAAAAA
6333341 AATAGGCG
66 AATAGGCG
* * *
6333349 TTACCTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTATTAATAATGTAAACGATAAAAA
1 CTACCTATTACATTAAAATACCTACCAGTTTTTTTGAAGGTTGTTAATAATGTAAACGAT-AAAA
**
6333414 AAATA-TTG
65 AAATAGGCG
* * *
6333422 CTACCTATTACATTAAAATACCTACCAGTTTTTTAGAAGGTTGCTAATAATGTAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCAGTTTTTTTGAAGGTTGTTAATAATGTAAACGATAAAAA
6333487 AATAGGCG
66 AATAGGCG
*
6333495 CTACCTATTACATTAAACTACCTACCAG
1 CTACCTATTACATTAAAATACCTACCAG
6333523 ATATGTTGAA
Statistics
Matches: 157, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
72 9 0.06
73 139 0.89
74 9 0.06
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (73 bp):
CTACCTATTACATTAAAATACCTACCAGTTTTTTTGAAGGTTGTTAATAATGTAAACGATAAAAA
AATAGGCG
Found at i:6333997 original size:114 final size:114
Alignment explanation
Indices: 6333602--6334201 Score: 844
Period size: 114 Copynumber: 5.3 Consensus size: 114
6333592 TAGTGCATAT
* *
6333602 AAAGTATCGATAC--TTTATAAAAATATATCGATACTTTACAATATAACAGGTAAAAATATGACA
1 AAAGTATTGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
*
6333665 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTAATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* *
6333714 AAAATATCGATAC--TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
1 AAAGTATTGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
*
6333777 AAACCAGTTTCATTATGA-AAAACCGGTAAAGAGATACCTGATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * * *
6333825 AAAGTATCGATAC--TTTAT-AAAATGTATCGATACTTTACAATATAATAGGTAAATATATGAAA
1 AAAGTATTGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
* *
6333887 AAACTAGTTTCATTATGACAAAACCGATAAAGAGCTACCTGATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * * *
6333936 AAAGTATTGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAGCATGTAAAAATATGATA
1 AAAGTATTGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
* *
6334001 AAACCAGTTTCATTATGACAAAACCGGTAAAAAACTACCTGATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * * * *
6334050 AAAGTATAT-ATACTTTTTATAAAAATGTATTGACACTTTACAATATAACATGTACAATTATGAC
1 AAAGTAT-TGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGAC
* * *
6334114 AAAACCAGTTTCAGTATGACAAAATCGGTAAAGAGCTACCTGATATGTTC
65 AAAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
** *
6334164 AAAGTATAT-ATACTTTTT-TGTACATGTATCGATACTTT
1 AAAGTAT-TGATACTTTTTATAAAAATGTATCGATACTTT
6334202 GTTGAAAGTA
Statistics
Matches: 444, Mismatches: 39, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
110 58 0.13
111 84 0.19
112 79 0.18
113 20 0.05
114 202 0.45
115 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (114 bp):
AAAGTATTGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACA
AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
Found at i:6334198 original size:22 final size:22
Alignment explanation
Indices: 6334173--6334242 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
6334163 CAAAGTATAT
6334173 ATACTTTTTTGTACATGTATCG
1 ATACTTTTTTGTACATGTATCG
* * **
6334195 ATACTTTGTTG-A-AAGTATAT
1 ATACTTTTTTGTACATGTATCG
6334215 ATAC-TTTTTGTACATGTATCG
1 ATACTTTTTTGTACATGTATCG
6334236 ATACTTT
1 ATACTTT
6334243 GTTGAAAGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 5 0.14
20 10 0.27
21 10 0.27
22 12 0.32
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (22 bp):
ATACTTTTTTGTACATGTATCG
Found at i:6334235 original size:41 final size:42
Alignment explanation
Indices: 6334159--6334251 Score: 170
Period size: 41 Copynumber: 2.2 Consensus size: 42
6334149 CTACCTGATA
*
6334159 TGTTCAAAGTATATATACTTTTTTGTACATGTATCGATACTT
1 TGTTGAAAGTATATATACTTTTTTGTACATGTATCGATACTT
6334201 TGTTGAAAGTATATATAC-TTTTTGTACATGTATCGATACTT
1 TGTTGAAAGTATATATACTTTTTTGTACATGTATCGATACTT
6334242 TGTTGAAAGT
1 TGTTGAAAGT
6334252 TATGTAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 33 0.66
42 17 0.34
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (42 bp):
TGTTGAAAGTATATATACTTTTTTGTACATGTATCGATACTT
Found at i:6334239 original size:21 final size:21
Alignment explanation
Indices: 6334173--6334242 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
6334163 CAAAGTATAT
6334173 ATACTTTTTTGTACATGTATCG
1 ATAC-TTTTTGTACATGTATCG
* **
6334195 ATACTTTGTTG-A-AAGTATAT
1 ATACTTT-TTGTACATGTATCG
6334215 ATACTTTTTGTACATGTATCG
1 ATACTTTTTGTACATGTATCG
6334236 ATACTTT
1 ATACTTT
6334243 GTTGAAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
19 3 0.08
20 13 0.33
21 16 0.41
22 7 0.18
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (21 bp):
ATACTTTTTGTACATGTATCG
Found at i:6336415 original size:259 final size:256
Alignment explanation
Indices: 6335807--6336442 Score: 627
Period size: 259 Copynumber: 2.5 Consensus size: 256
6335797 GATAATGTAA
* ** * *
6335807 TTCCACCTCCTTCTATGATGGAAATGAACAAAAGGTTG-CATTGATCTACCTCATATTGTGGTAG
1 TTCCACCTCCTTCTATGATGGAAATGAGCAAAAGGTTGACGCTGATCTACCTCATATTATGATAG
* * * *
6335871 AATCAAACGCATCATA-GGTGCTGATCTACATTGTGATGTGATAGAATCGAGAAAATTGACCATA
66 AATCAAATGCAACA-AGGGTGCTGATCTACCTTGTGATGTGATAGAATCGAGAAAATCGACCATA
* * * *
6335935 TTGATCCACCTTATTCTGTAACAAACAAACAAAATGTTAACACTGACCCACCTCCTATTATGATG
130 TTCATCCACATTATTCTGTAACAAACAAACAAAATGTCAACACTGACCCACCTCCTATTATAATG
* * *
6336000 GAGTAAAAAAATGTGGTAATCCAAATCTTTATGCGATGAAATCGAGCATAAGGGTAATGTTG
195 GAGTAAAAAAATGTGGTAATCCAAATCTCTATGCGATGAAATCGAGCACAAGAGTAATGTTG
* * * * * * * * * *
6336062 TTTCATCTCCTTCAATGATAGAAATGGGCAAAAGGTTGATGCTGGTCTTCCTCCTACTATGATAG
1 TTCCACCTCCTTCTATGATGGAAATGAGCAAAAGGTTGACGCTGATCTACCTCATATTATGATAG
* * * * * * *
6336127 AATCAAATGCAAAAAGGATGCTAATCTACCTTTTGTTGTGATAGAATTGAGTAAAA-CGACCATG
66 AATCAAATGCAACAAGGGTGCTGATCTACCTTGTGATGTGATAGAATCGAG-AAAATCGACCATA
* * * *** * ** *
6336191 TTCATCCACATTCTTTTGTGATGGACGAACAAAATGTCAACGTTGACCCACCTCCTATTGTAATG
130 TTCATCCACATTATTCTGTAACAAACAAACAAAATGTCAACACTGACCCACCTCCTATTATAATG
* * * * * * * * *
6336256 GAGTTAAGCAAATTAGTGTTGATCTAACTC-CTACTGTGATGGAATCGAGCACAATAGTAATGTT
195 GAG-TAA-AAAAAT-GTGGTAATCCAAATCTCTA-TGCGATGAAATCGAGCACAAGAGTAATGTT
6336320 G
256 G
* *
6336321 TTCCACCTCTTTCTGTGATGGAAATGAGCATAAA-GTTGACGCTGATCTACCTCATATTATGATA
1 TTCCACCTCCTTCTATGATGGAAATGAGCA-AAAGGTTGACGCTGATCTACCTCATATTATGATA
* * **
6336385 AAATCAAATGCAACAAGGGTGTTGATCTACCTCCT-ACTGTGATAGAATCGAGCAAAAT
65 GAATCAAATGCAACAAGGGTGCTGATCTACCTTGTGA-TGTGATAGAATCGAG-AAAAT
6336443 GATCATGTTG
Statistics
Matches: 297, Mismatches: 74, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
255 33 0.11
256 117 0.39
257 7 0.02
258 6 0.02
259 131 0.44
260 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (256 bp):
TTCCACCTCCTTCTATGATGGAAATGAGCAAAAGGTTGACGCTGATCTACCTCATATTATGATAG
AATCAAATGCAACAAGGGTGCTGATCTACCTTGTGATGTGATAGAATCGAGAAAATCGACCATAT
TCATCCACATTATTCTGTAACAAACAAACAAAATGTCAACACTGACCCACCTCCTATTATAATGG
AGTAAAAAAATGTGGTAATCCAAATCTCTATGCGATGAAATCGAGCACAAGAGTAATGTTG
Found at i:6336623 original size:126 final size:126
Alignment explanation
Indices: 6336480--6337557 Score: 799
Period size: 126 Copynumber: 8.6 Consensus size: 126
6336470 ATAGACGAGT
* * * * * * *
6336480 GAAACCACCATGTTGATCGACTTCCTTCTATGATGGACGGACAAAGGATTATGCTGATCTAACTA
1 GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACTA
* * * * *
6336545 CTATTATGTTGGAAAAGTAAAAATGACTACGCTGATCCAACCCATTCCTCGATGGATGAGC
66 CTATTATGCTGGAAAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATGAGC
* * * * * *
6336606 GAAACCGCCATGTTGATCCACCTTCTTCTATGATGGATGAACAAAAGATTACGCTGACTCAACTA
1 GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACTA
* * ** * * * * * * ** * *
6336671 CTAGT-TGTTATATGAA-CGAAAATGACTACATTAATCCAACCCCTTATTTGATAAAAGAGA
66 CTATTATGCTGGA-AAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATGAGC
* * * ** *
6336731 AAAACCATCATGTTGAT-CATCCTCATTCTACGATGGACAAACAAAGGATTACGCTGACCCAACT
1 GAAACCACCATGTTGATCCA-CCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACT
* * * * * * * *
6336795 ACTATTTTGTTGGACAAAAG-AAGAATGAATAC-TATAAACCAACCCCTTATTTGATGGAAT-AG
65 ACTATTATGCTGG--AAAAGCAAAAATGACTACGT-TGATCCAACCCCTTCTTCGATGG-ATGAG
6336857 C
126 C
* * * * **
6336858 GAAATCACCATGTTGATCCACCTCCTTATGTAATGGACAAACAAAGGATTACATTGACCCAACTA
1 GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACTA
* * ** * * ** * * * * *
6336923 CTAATATGCTAGACGAGCGAAAATGATTGTGTTGATCTAACCACTTATTCAATGGACGAGC
66 CTATTATGCTGGAAAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATGAGC
* * * * *
6336984 GAAACCACCATGTTGATCCACCTCCTTTTGCGATGGACGAACAAAAGATTACTCTGACCTAACTA
1 GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACTA
* ** ** ** *
6337049 CTAATATGCTGGACAAA-CTGAAATGACTACAATGATCCAACCCCTTCTTTAATGGATGCA-T
66 CTATTATGCTGGA-AAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATG-AGC
* * * * * ** *
6337110 AAAACCACCATGTAGA-CCTACCTCCTTTTTTGATGGATGAGTAAAGGATTACGTTGACCCAACT
1 GAAACCACCATGTTGATCC-ACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACT
* ** * * ** *
6337174 ACTATTGTGCTGGATGAGCAAAAATGACTACGTTGATCCAACCCCCTCTTCGATAGACAATC
65 ACTATTATGCTGGAAAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATGAGC
* * *
6337236 GAAACCTCCATGTTGATCCACCTCCTTCTTTGATGGACGAACAAAGGATTA-GACTGATCCAACT
1 GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACG-CTGACCCAACT
* ** ** * * ** *
6337300 ACTATTGTGCTGGACGAGCGGAAATGACTACGCTGATCCAACCCCCTCTTCGATATATAAGC
65 ACTATTATGCTGGAAAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATGAGC
* * ** ** * * * * * * * *
6337362 AAAACCACCATATTGATTAACCTTTTTTTGTGATTGATGAATAAGGGATTACACTGATCCAACTG
1 GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACTA
** * * * * ** *
6337427 CTGGTGTGTTGGACAAGCAAAAATGACTACGTTGATCCAATCTTTTCTTCGATGGATGAGT
66 CTATTATGCTGGAAAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATGAGC
* * *
6337488 GAAACAACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACCCTGACCTAACTA
1 GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACTA
6337553 CTATT
66 CTATT
6337558 GTGATAGACG
Statistics
Matches: 739, Mismatches: 193, Indels: 40
0.76 0.20 0.04
Matches are distributed among these distances:
124 2 0.00
125 101 0.14
126 534 0.72
127 98 0.13
128 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (126 bp):
GAAACCACCATGTTGATCCACCTCCTTCTGTGATGGACGAACAAAGGATTACGCTGACCCAACTA
CTATTATGCTGGAAAAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATGGATGAGC
Found at i:6337122 original size:252 final size:250
Alignment explanation
Indices: 6336433--6337557 Score: 900
Period size: 252 Copynumber: 4.5 Consensus size: 250
6336423 GTGATAGAAT
* * * * * *
6336433 CGAGC-AAAATGA-TCATGTTGATCTATCCCCTTCTACAATAGACGAGTGAAACCACCATGTTGA
1 CGAGCAAAAATGACT-ACGTTGATCCAACCCCTTCTTCGATAGACGAGCGAAACCACCATGTTGA
* * * * *
6336496 TCGACTTCCTTCTATGATGGACGGACAAAGGATTA-TGCTGATCTAACTACTATTATGTTGGA-A
65 TCCACCTCCTTCTATGATGGACGAACAAAGGATTACT-CTGACCTAACTACTATTATGCTGGACA
* * * * * ** * *
6336559 AAGTAAAAATGACTACGCTGATCCAACCCATTCCTCGATGGATGAGCGAAACCGCCATGTTGATC
129 AACT-GAAATGACTACGATGATCCAACCCCTTCTTTAATGGAT--GCAAAACCACCATGTTGATC
* * * * * * * *
6336624 CACCTTCTTCTATGATGGATGAACAAAAGATTACGCTGACTCAACTACTAGT-TGTTATA
191 CACCTCCTTTTGTGATGGATGAACAAAGGATTACACTGACCCAACTACTAGTGTGCTAGA
* * * * * * * * * ** *
6336683 TGAACGAAAATGACTACATTAATCCAACCCCTTATTTGATAAAAGAGAAAAACCATCATGTTGAT
1 CGAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATAGACGAGCGAAACCACCATGTTGAT
* * * * * * *
6336748 -CATCCTCATTCTACGATGGACAAACAAAGGATTACGCTGACCCAACTACTATTTTGTTGGACAA
66 CCA-CCTCCTTCTATGATGGACGAACAAAGGATTACTCTGACCTAACTACTATTATGCTGGACAA
* * * * * * * * *
6336812 A-AGAAGAATGAATACTATAAACCAACCCCTTATTTGATGGAATAGCGAAATCACCATGTTGATC
130 ACTG-A-AATGACTACGATGATCCAACCCCTTCTTTAATGG-AT-GCAAAACCACCATGTTGATC
* * ** * * *
6336876 CACCTCCTTATGTAATGGACAAACAAAGGATTACATTGACCCAACTACTAATATGCTAGA
191 CACCTCCTTTTGTGATGGATGAACAAAGGATTACACTGACCCAACTACTAGTGTGCTAGA
* * ** * * * * *
6336936 CGAGCGAAAATGATTGTGTTGATCTAACCACTTATTCAATGGACGAGCGAAACCACCATGTTGAT
1 CGAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATAGACGAGCGAAACCACCATGTTGAT
* ** * *
6337001 CCACCTCCTTTTGCGATGGACGAACAAAAGATTACTCTGACCTAACTACTAATATGCTGGACAAA
66 CCACCTCCTTCTATGATGGACGAACAAAGGATTACTCTGACCTAACTACTATTATGCTGGACAAA
* *
6337066 CTGAAATGACTACAATGATCCAACCCCTTCTTTAATGGATGCATAAAACCACCATGTAGA-CCTA
131 CTGAAATGACTACGATGATCCAACCCCTTCTTTAATGGATGC--AAAACCACCATGTTGATCC-A
* ** ** * *
6337130 CCTCCTTTTTTGATGGATGAGTAAAGGATTACGTTGACCCAACTACTATTGTGCTGGA
193 CCTCCTTTTGTGATGGATGAACAAAGGATTACACTGACCCAACTACTAGTGTGCTAGA
* * * * *
6337188 TGAGCAAAAATGACTACGTTGATCCAACCCCCTCTTCGATAGACAATCGAAACCTCCATGTTGAT
1 CGAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATAGACGAGCGAAACCACCATGTTGAT
* ** * *
6337253 CCACCTCCTTCTTTGATGGACGAACAAAGGATTAGACTGATCC-AACTACTATTGTGCTGGACGA
66 CCACCTCCTTCTATGATGGACGAACAAAGGATTACTCTGA-CCTAACTACTATTATGCTGGACAA
* * * * * ** * * **
6337317 GCGGAAATGACTACGCTGATCCAACCCCCTCTTCGATATATAAGCAAAACCACCATATTGATTAA
130 ACTGAAATGACTACGATGATCCAACCCCTTCTT-TA-ATGGATGCAAAACCACCATGTTGATCCA
** * * * * * * * *
6337382 CCTTTTTTTGTGATTGATGAATAAGGGATTACACTGATCCAACTGCTGGTGTGTTGGA
193 CCTCCTTTTGTGATGGATGAACAAAGGATTACACTGACCCAACTACTAGTGTGCTAGA
* * ** * * * *
6337440 CAAGCAAAAATGACTACGTTGATCCAATCTTTTCTTCGATGGATGAGTGAAACAACCATGTTGAT
1 CGAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATAGACGAGCGAAACCACCATGTTGAT
* *
6337505 CCACCTCCTTCTGTGATGGACGAACAAAGGATTACCCTGACCTAACTACTATT
66 CCACCTCCTTCTATGATGGACGAACAAAGGATTACTCTGACCTAACTACTATT
6337558 GTGATAGACG
Statistics
Matches: 691, Mismatches: 165, Indels: 36
0.77 0.18 0.04
Matches are distributed among these distances:
250 6 0.01
251 98 0.14
252 468 0.68
253 111 0.16
254 8 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (250 bp):
CGAGCAAAAATGACTACGTTGATCCAACCCCTTCTTCGATAGACGAGCGAAACCACCATGTTGAT
CCACCTCCTTCTATGATGGACGAACAAAGGATTACTCTGACCTAACTACTATTATGCTGGACAAA
CTGAAATGACTACGATGATCCAACCCCTTCTTTAATGGATGCAAAACCACCATGTTGATCCACCT
CCTTTTGTGATGGATGAACAAAGGATTACACTGACCCAACTACTAGTGTGCTAGA
Found at i:6341052 original size:54 final size:54
Alignment explanation
Indices: 6341024--6342987 Score: 2534
Period size: 54 Copynumber: 36.4 Consensus size: 54
6341014 TATAATTTAT
*
6341024 GTGGGTTGCACACATAGTGTCTAAACGGTTGTTCATCAACATATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * **
6341078 GTGGATTGCACACATAGTTCCTAAATGGTTGTTCATCAACATATGATGAATTTT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * * ** *
6341132 ATGGGATACACACATAGTGCCTAAAGGGTAATTCATCAACATATGATGAATTCT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * * *
6341186 GTGGCTTTCA-ACATAGTGCCTAAATGGTTGTTCATCTACATATGATAAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * * * **
6341239 GTGGGTTGCACAAATATTTCCTAAACGGTTATTCATCAACATGTGATGAATTTT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
*
6341293 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAATATATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* *
6341347 GTGGGTTGCACACATAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTAC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * *
6341401 GTGGGTTGCACACATAATGCCTAAACGGTTGTTTATCAACATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * *
6341455 GTGGGTTGCACACATAGTGCCTAAATGGTTATTCATCAACATATGATGAAATCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* ** *
6341509 GTGGGTTGCACACATAGTGCCTAAACGGTTTTTCATCAGTATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * *
6341563 GTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACATATAATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
*** * * *
6341617 GTGGGAAACACACGTAGTGCCTAAACGATTGTTCATCAACATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * *
6341671 GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAATATATGATGAA-TCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * * *
6341724 GTGGATTGCACACATAGTGCCCAAATGGTTGTTCATCAACATATGATAAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * * * * * * *
6341778 GCGTGTTACACAAATAATGCCTAAACGATTATTCGTCAACATATGATGAATTCT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * ** * *
6341832 GTTGGTTGCACACATAGTACCTAAACAATTGTTCATTAACATATGATGAATTCT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* *
6341886 GTGGGTTGCACACATAGTGTCTAAACTGTTGTTCATCAACATATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* *
6341940 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
6341994 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * *
6342048 ATGGATTGCTCACATAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * *
6342102 GTGGATTGCTCACATAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* ** * **
6342156 GTGGGTTGCACACATAGTGCCTAAACGGTTTTTCATCAGTATATGATGCATTTA
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * **
6342210 GTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACATATTATGAATTTT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * *
6342264 GTGGGTTGCACACGTAGTGCCTAAATGATTGTTCATCAACATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* *
6342318 GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAACATATGATGAA-TCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * * **
6342371 GTGGATTGCACACATAGTGCCCAGACGGTTGTTCATCAACATATGATAAATTTT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* ** * * * * **
6342425 GTGTGTTATACAAATAATGCCTAAACGATTGTTCGTCAACATATGATGAATTAT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* ** * *
6342479 GTGGGTTGCACACATAGTGCGTAAACAATTGTTCATTAACATATGATGAATTCT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* ** * * * *
6342533 GTGGGTTTCATGCATAGTGTCTAAACTGTTGGTCATCAACATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* *
6342587 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATTTC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* *
6342641 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTTATCAAAATATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * **
6342695 GTGGATTGCTCACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTTT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* *
6342749 GTGTGTTGCACACATAGTGCCTAAACGGTTGTTCATCAATATATGATGAATAT-C
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAAT-TCC
* * *
6342803 GTGGGTTGCACACATAGTGCCTAAACAGTTGTTCATCAATATATAATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * *
6342857 GTGAGTTGCACACATAGTGCCTAAACGGTTTTTCATCAATATATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
* * * **
6342911 ATGGATTGCACACATAGTGTCTAAACGGTTGTTCAT-AACCATATGATGAATTTT
1 GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAA-CATATGATGAATTCC
*
6342965 GTGGGTTGAACACATAGTGCCTA
1 GTGGGTTGCACACATAGTGCCTA
6342988 TAGTACACAT
Statistics
Matches: 1657, Mismatches: 247, Indels: 12
0.86 0.13 0.01
Matches are distributed among these distances:
53 141 0.09
54 1515 0.91
55 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (54 bp):
GTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCC
Found at i:6341900 original size:27 final size:27
Alignment explanation
Indices: 6341870--6341955 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
6341860 TTGTTCATTA
6341870 ACATATGATGAATTCTGTGGGTTGCAC
1 ACATATGATGAATTCTGTGGGTTGCAC
* * *
6341897 ACATAGTG-TCTAA-ACTGT-TGTT-CATC
1 ACATA-TGAT-GAATTCTGTGGGTTGCA-C
*
6341923 AACATATGATGAATTCCGTGGGTTGCAC
1 -ACATATGATGAATTCTGTGGGTTGCAC
6341951 ACATA
1 ACATA
6341956 GTGCCTAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 2 0.05
26 8 0.18
27 24 0.55
28 8 0.18
29 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (27 bp):
ACATATGATGAATTCTGTGGGTTGCAC
Found at i:6342089 original size:27 final size:27
Alignment explanation
Indices: 6342059--6342144 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
6342049 TGGATTGCTC
6342059 ACATAGTGCCTAAATGGTTGTTCATCA
1 ACATAGTGCCTAAATGGTTGTTCATCA
* * * *
6342086 ACATA-TG-ATGAATTCCGTGGATTGC-TC-
1 ACATAGTGCCT-AAAT-GGTTG-TT-CATCA
6342113 ACATAGTGCCTAAATGGTTGTTCATCA
1 ACATAGTGCCTAAATGGTTGTTCATCA
6342140 ACATA
1 ACATA
6342145 TGATGAATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 2 0.05
26 9 0.21
27 21 0.49
28 9 0.21
29 2 0.05
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
ACATAGTGCCTAAATGGTTGTTCATCA
Found at i:6342261 original size:647 final size:646
Alignment explanation
Indices: 6341024--6342985 Score: 2982
Period size: 647 Copynumber: 3.0 Consensus size: 646
6341014 TATAATTTAT
* * *
6341024 GTGGGTTGCACACATAGTGTCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGATTGCAC
1 GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAACATATGATGAA-TCCGTGGATTGCAC
* * * * * * * *
6341089 ACATAGTTCCTAAATGGTTGTTCATCAACATATGATGAATTTTATGGGATACACACATAGTGCCT
65 ACATAGTGCCCAAATGGTTGTTCATCAACATATGATAAATTTTGTGTGTTACACAAATAATGCCT
* * * * * ***
6341154 AAAGGGTAATTCATCAACATATGATGAATTCTG-TGGCTTTCA-ACATAGTGCCTAAATGGTTGT
130 AAACGATTATTCGTCAACATATGATGAATTCTGTTGG-TTGCACACATAGTGCCTAAACAATTGT
* * * * * *
6341217 TCATCT-ACATATGATAAATTCCGTGGGTTGCACAAATA-TTTCCTAAACGGTTATTCATCAACA
194 TCAT-TAACATATGATGAATTCTGTGGGTTGCACACATAGTGT-CTAAACTGTTGTTCATCAACA
* * * *
6341280 TGTGATGAATTTTGTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAATATATGATGAATT
257 TATGATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATT
* * * *
6341345 CCGTGGGTTGCACACATAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTACGTGGGTTGC
322 TCGTGGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGATTGC
* * *
6341410 ACACATAATGCCTAAACGGTTGTTTATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGC
387 TCACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTTCGT-GGTTGCACACATAGTGC
* * *
6341475 CTAAATGGTTATTCATCAACATATGATGAAATCCGTGGGTTGCACACATAGTGCCTAAACGGTTT
451 CTAAATGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTT
6341540 TTCATCAGTATATGATGAATTTCGTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACAT
516 TTCATCAGTATATGATGAATTTCGTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACAT
**
6341605 ATAATGAATTTCGTGGGAAACACACGTAGTGCCTAAACGATTGTTCATCAACATATGATGAATTT
581 ATAATGAATTTCGTGGGATGCACACGTAGTGCCTAAACGATTGTTCATCAACATATGATGAATTT
6341670 C
646 C
*
6341671 GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAATATATGATGAATCCGTGGATTGCACA
1 GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAACATATGATGAATCCGTGGATTGCACA
* *
6341736 CATAGTGCCCAAATGGTTGTTCATCAACATATGATAAATTTCGCGTGTTACACAAATAATGCCTA
66 CATAGTGCCCAAATGGTTGTTCATCAACATATGATAAATTTTGTGTGTTACACAAATAATGCCTA
*
6341801 AACGATTATTCGTCAACATATGATGAATTCTGTTGGTTGCACACATAGTACCTAAACAATTGTTC
131 AACGATTATTCGTCAACATATGATGAATTCTGTTGGTTGCACACATAGTGCCTAAACAATTGTTC
6341866 ATTAACATATGATGAATTCTGTGGGTTGCACACATAGTGTCTAAACTGTTGTTCATCAACATATG
196 ATTAACATATGATGAATTCTGTGGGTTGCACACATAGTGTCTAAACTGTTGTTCATCAACATATG
*
6341931 ATGAATTCCGTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATTTCGT
261 ATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATTTCGT
*
6341996 GGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCATGGATTGCTCAC
326 GGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGATTGCTCAC
* * *
6342061 ATAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTCCGTGGATTGCTCACATAGTGCCTAA
391 ATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTTCGTGG-TTGCACACATAGTGCCTAA
6342126 ATGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTTTTCA
455 ATGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTTTTCA
* * *
6342191 TCAGTATATGATGCATTTAGTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACATATTA
520 TCAGTATATGATGAATTTCGTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACATATAA
* * *
6342256 TGAATTTTGTGGGTTGCACACGTAGTGCCTAAATGATTGTTCATCAACATATGATGAATTTC
585 TGAATTTCGTGGGATGCACACGTAGTGCCTAAACGATTGTTCATCAACATATGATGAATTTC
6342318 GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAACATATGATGAATCCGTGGATTGCACA
1 GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAACATATGATGAATCCGTGGATTGCACA
* * *
6342383 CATAGTGCCCAGACGGTTGTTCATCAACATATGATAAATTTTGTGTGTTATACAAATAATGCCTA
66 CATAGTGCCCAAATGGTTGTTCATCAACATATGATAAATTTTGTGTGTTACACAAATAATGCCTA
* * * *
6342448 AACGATTGTTCGTCAACATATGATGAATTATGTGGGTTGCACACATAGTGCGTAAACAATTGTTC
131 AACGATTATTCGTCAACATATGATGAATTCTGTTGGTTGCACACATAGTGCCTAAACAATTGTTC
* ** *
6342513 ATTAACATATGATGAATTCTGTGGGTTTCATGCATAGTGTCTAAACTGTTGGTCATCAACATATG
196 ATTAACATATGATGAATTCTGTGGGTTGCACACATAGTGTCTAAACTGTTGTTCATCAACATATG
6342578 ATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATTTCGT
261 ATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATTTCGT
* *
6342643 GGGTTGCACACATAGTGCCTAAACGGTTGTTTATCAAAATATGATGAATTCCGTGGATTGCTCAC
326 GGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGATTGCTCAC
*
6342708 ATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTTTGTGTGTTGCACACATAGTGCCTAA
391 ATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTTCGTG-GTTGCACACATAGTGCCTAA
* * * * *
6342773 ACGGTTGTTCATCAATATATGATGAATATCGTGGGTTGCACACATAGTGCCTAAACAGTTGTTCA
455 ATGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTTTTCA
* * * * * * * * *
6342838 TCAATATATAATGAATTCCGTGAGTTGCACACATAGTGCCTAAACGGTTTTTCATCAATATATGA
520 TCAGTATATGATGAATTTCGTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACATATAA
* * * * * *
6342903 TGAATTCCAT-GGATTGCACACATAGTGTCTAAACGGTTGTTCAT-AACCATATGATGAATTTT
585 TGAATTTCGTGGGA-TGCACACGTAGTGCCTAAACGATTGTTCATCAA-CATATGATGAATTTC
*
6342965 GTGGGTTGAACACATAGTGCC
1 GTGGGTTGCACACATAGTGCC
6342986 TATAGTACAC
Statistics
Matches: 1202, Mismatches: 105, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
646 109 0.09
647 1090 0.91
648 3 0.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (646 bp):
GTGGGTTGCACACATAGTGCCGAAACAGTTGTTCATCAACATATGATGAATCCGTGGATTGCACA
CATAGTGCCCAAATGGTTGTTCATCAACATATGATAAATTTTGTGTGTTACACAAATAATGCCTA
AACGATTATTCGTCAACATATGATGAATTCTGTTGGTTGCACACATAGTGCCTAAACAATTGTTC
ATTAACATATGATGAATTCTGTGGGTTGCACACATAGTGTCTAAACTGTTGTTCATCAACATATG
ATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTGTTAATCAACATATGATGAATTTCGT
GGGTTGCACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGATTGCTCAC
ATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTTCGTGGTTGCACACATAGTGCCTAAA
TGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTAAACGGTTTTTCAT
CAGTATATGATGAATTTCGTGGGTTGTACACATAGTGCCTAAACAGTTGTTCATCAACATATAAT
GAATTTCGTGGGATGCACACGTAGTGCCTAAACGATTGTTCATCAACATATGATGAATTTC
Found at i:6343454 original size:19 final size:20
Alignment explanation
Indices: 6343411--6343459 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
6343401 GTAATCAATG
*
6343411 GTATCGATACCTTCTCCCTA
1 GTATCGATACCCTCTCCCTA
*
6343431 GTATCGATACCCTCTCTC-A
1 GTATCGATACCCTCTCCCTA
6343450 GTATCGATAC
1 GTATCGATAC
6343460 TAATTGCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.22, C:0.33, G:0.12, T:0.33
Consensus pattern (20 bp):
GTATCGATACCCTCTCCCTA
Found at i:6348382 original size:54 final size:54
Alignment explanation
Indices: 6348355--6348747 Score: 561
Period size: 54 Copynumber: 7.3 Consensus size: 54
6348345 ATGTGGGCTA
* * *
6348355 CACACATAGTGCCTAAACAGTTGTTCATCAACATACGATGAATTCTGTGGGTTG
1 CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
* *
6348409 CACACATAGAGCCTAAACGGTTGTTCATCAACATATGATGAATTCCATGGGTTG
1 CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
* * * *
6348463 CACACACAGTGCCTAAATGGTTGTTCATTAACATATGATGAATTCTGTGGGTTG
1 CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
* * *
6348517 CACACATAGTGCCTAAACGGTTGTTCATTAACATATGATGAATTCCGTGGATTA
1 CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
* * * *
6348571 CACACATAGTTCCTAAGCGGTTGTTCATCAACATATGATGAATTTCGTGTGTTG
1 CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
* * *
6348625 GACACATAGTGCCTAAATGGTTGTTCATCAACATATGATGAATTCCGTGGATTG
1 CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
* * * * *
6348679 TACACATAGTGCCTAAATGGTTGTTCATTAACATATGATGAATTTCGTGGGTTA
1 CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
*
6348733 CATACATAGTGCCTA
1 CACACATAGTGCCTA
6348748 TAGTACACAT
Statistics
Matches: 302, Mismatches: 37, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 302 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (54 bp):
CACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTG
Found at i:6349206 original size:19 final size:20
Alignment explanation
Indices: 6349163--6349211 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6349153 GTAATCAATG
** *
6349163 GTATCGATACTTTCTCTATA
1 GTATCGATACCCTCTCTACA
6349183 GTATCGATACCCTCTCT-CA
1 GTATCGATACCCTCTCTACA
*
6349202 GTATCAATAC
1 GTATCGATAC
6349212 TAATTGCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (20 bp):
GTATCGATACCCTCTCTACA
Found at i:6354175 original size:21 final size:21
Alignment explanation
Indices: 6354148--6354235 Score: 124
Period size: 21 Copynumber: 4.2 Consensus size: 21
6354138 CTTCAGGGAA
6354148 ACTTACCAAGGTACTTCA-CTT
1 ACTTACCAAGGTACTTCATC-T
*
6354169 ATTTACCAAGGTACTTCATCT
1 ACTTACCAAGGTACTTCATCT
*
6354190 ACTTACCAAGATACTTCATCT
1 ACTTACCAAGGTACTTCATCT
* *
6354211 ACTTACTAAGGTAATTCATCT
1 ACTTACCAAGGTACTTCATCT
6354232 ACTT
1 ACTT
6354236 CCACTTTTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 59 0.98
22 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (21 bp):
ACTTACCAAGGTACTTCATCT
Found at i:6354429 original size:114 final size:113
Alignment explanation
Indices: 6354223--6354443 Score: 309
Period size: 114 Copynumber: 1.9 Consensus size: 113
6354213 TTACTAAGGT
* * * * *
6354223 AATTCATCTACTTCCACTTTTCTTCTACTCCATCTTCTACCACGAATACTGAATCAGGCAATGAC
1 AATTAATCTACTTCCACTTTTCTTCTACTCCACCTTCTACCAAGAATACTAAATCAGACAATGAC
*
6354288 ATCGATGAATACGATGCTAGCAACATTGTAATATAAGATACCCAATGC
66 ATCGATGAATACGATGCTAGCAACATTGTAATAGAAGATACCCAATGC
** * * *
6354336 AATTAATCTACTTCCACTTTTTCTTCTACTTGACCTTCTACCAAGGATACTAAATTAGATAATGA
1 AATTAATCTACTTCCAC-TTTTCTTCTACTCCACCTTCTACCAAGAATACTAAATCAGACAATGA
*
6354401 CATCGATGAATACGATTCTAG-AAGCATTGTAATAGAAGATACC
65 CATCGATGAATACGATGCTAGCAA-CATTGTAATAGAAGATACC
6354444 AATCTTCCCT
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
113 18 0.19
114 76 0.81
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (113 bp):
AATTAATCTACTTCCACTTTTCTTCTACTCCACCTTCTACCAAGAATACTAAATCAGACAATGAC
ATCGATGAATACGATGCTAGCAACATTGTAATAGAAGATACCCAATGC
Found at i:6364453 original size:90 final size:89
Alignment explanation
Indices: 6364298--6364461 Score: 301
Period size: 90 Copynumber: 1.8 Consensus size: 89
6364288 TAACACACCC
6364298 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATT
6364363 TAATTAATTGGAATTTAATAATCA
66 TAATTAATTGGAATTTAATAATCA
* *
6364387 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATATAT
6364452 TTAATTAATT
65 TTAATTAATT
6364462 AAAACTAAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 32 0.44
90 40 0.56
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATT
TAATTAATTGGAATTTAATAATCA
Found at i:6364502 original size:20 final size:21
Alignment explanation
Indices: 6364434--6364503 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
6364424 TATTATTTCA
*
6364434 AATTAATTAAATC-TATATTT
1 AATTAATTAAAACATATATTT
* *
6364454 AATTAATTAAAACTAAATATTCGG
1 AATTAATTAAAAC-ATATATT--T
*
6364478 GATT-ATTAAAACATATATTT
1 AATTAATTAAAACATATATTT
6364498 AATTAA
1 AATTAA
6364504 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 15 0.39
21 1 0.03
22 11 0.29
23 8 0.21
24 3 0.08
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (21 bp):
AATTAATTAAAACATATATTT
Found at i:6369013 original size:21 final size:21
Alignment explanation
Indices: 6368989--6369028 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6368979 AGATAGAAAC
*
6368989 GATTTTGTGTGAAAAGAGCAT
1 GATTTTGTATGAAAAGAGCAT
6369010 GATTTTGTATGAAAAGAGC
1 GATTTTGTATGAAAAGAGC
6369029 CTGTTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (21 bp):
GATTTTGTATGAAAAGAGCAT
Found at i:6370792 original size:16 final size:16
Alignment explanation
Indices: 6370771--6370802 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6370761 AAAGCATGAC
6370771 TGGGTAGATACCATGT
1 TGGGTAGATACCATGT
*
6370787 TGGGTAGATATCATGT
1 TGGGTAGATACCATGT
6370803 GAATAAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.34
Consensus pattern (16 bp):
TGGGTAGATACCATGT
Found at i:6380766 original size:8 final size:8
Alignment explanation
Indices: 6380747--6380810 Score: 58
Period size: 8 Copynumber: 7.5 Consensus size: 8
6380737 AAAATGAATA
6380747 AAAAAATG
1 AAAAAATG
6380755 -AAAAATG
1 AAAAAATG
*
6380762 AAAAATAATAA
1 -AAAA-AAT-G
6380773 AAAATACATG
1 AAAA-A-ATG
6380783 AAAAAATG
1 AAAAAATG
6380791 AAAAAATG
1 AAAAAATG
*
6380799 AAAAAAAG
1 AAAAAATG
6380807 AAAA
1 AAAA
6380811 GAAACAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.15
8 22 0.46
9 4 0.08
10 13 0.27
11 2 0.04
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:6380805 original size:11 final size:11
Alignment explanation
Indices: 6380721--6380759 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6380711 TTTTTCTTGA
*
6380721 AAAAAAAAAGG
1 AAAAAAAAATG
*
6380732 AAGAAAAAATG
1 AAAAAAAAATG
6380743 AATAAAAAAATG
1 AA-AAAAAAATG
6380755 AAAAA
1 AAAAA
6380760 TGAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:6382020 original size:55 final size:56
Alignment explanation
Indices: 6381832--6382040 Score: 151
Period size: 55 Copynumber: 3.8 Consensus size: 56
6381822 AACGATCATT
* * * * * *
6381832 GAAGATTGTTCGAG-TCTTATACTCTCT-AAAGAAATAGGGAGCAGACACAATCGTCA
1 GAAGATTATTCGAGTTC-TATACTCCCTGAAAGAAAGAGGGAGCAAAC-CAATAGGCA
* * * ** * **
6381888 -AAGATTATTCGAGTTCTATACTTCCTGAAAGGAAGAGGAAGTGAACCCATTCGCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCAATAGGCA
* * ** *
6381943 GAAGATTATTTGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCAAACCTGTAGGAA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCAATAGGCA
* * *
6381998 GAAGATTGTTCGAG-TCTTATACTCTCTGAAA-AAATAGGGAGCA
1 GAAGATTATTCGAGTTC-TATACTCCCTGAAAGAAAGAGGGAGCA
6382041 GACATGATTA
Statistics
Matches: 118, Mismatches: 30, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
54 2 0.02
55 75 0.64
56 41 0.35
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (56 bp):
GAAGATTATTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCAATAGGCA
Found at i:6382066 original size:55 final size:55
Alignment explanation
Indices: 6381998--6382301 Score: 332
Period size: 55 Copynumber: 5.5 Consensus size: 55
6381988 CCTGTAGGAA
* ** *
6381998 GAAGATTGTTCGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACATGATTATT
1 GAAGATAGTTCGAGTCTTATACTCTCTGAACGAATAGGGAGCAGACACGATTATT
* * * *
6382053 AAAAATCAG-TCGAGTCTTATACTCTCTGAACGAATAAGGAGCAGACACGATTACT
1 GAAGAT-AGTTCGAGTCTTATACTCTCTGAACGAATAGGGAGCAGACACGATTATT
* * * * *
6382108 GAAGATTGTTCGAGT-TCTATACTCCCTGAAGGAATAGGGAGGAGACACGATTGTT
1 GAAGATAGTTCGAGTCT-TATACTCTCTGAACGAATAGGGAGCAGACACGATTATT
* *
6382163 GAAGATTA-TTCGAGTCTTATACTCTCTGAACGAATAGAGG-GCAGACATGATTGTT
1 GAAGA-TAGTTCGAGTCTTATACTCTCTGAACGAATAG-GGAGCAGACACGATTATT
* * *
6382218 GAAGATTGTTCGAGTCTTACACTCTCTGAA-GAAATAGGGAGCAGACACGATTGTT
1 GAAGATAGTTCGAGTCTTATACTCTCTGAACG-AATAGGGAGCAGACACGATTATT
* * *
6382273 GAAGA-CGTTCGAGTTTTATACTCCCTGAA
1 GAAGATAGTTCGAGTCTTATACTCTCTGAA
6382302 GAAAGAGGGA
Statistics
Matches: 211, Mismatches: 29, Indels: 19
0.81 0.11 0.07
Matches are distributed among these distances:
54 26 0.12
55 180 0.85
56 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (55 bp):
GAAGATAGTTCGAGTCTTATACTCTCTGAACGAATAGGGAGCAGACACGATTATT
Found at i:6382115 original size:110 final size:110
Alignment explanation
Indices: 6381998--6382310 Score: 386
Period size: 110 Copynumber: 2.9 Consensus size: 110
6381988 CCTGTAGGAA
* *
6381998 GAAGATTGTTCGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACATGATTATTAAAAATCAGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTAAAAATCAGT
6382063 CGAGTCTTATACTCTCTGAACGAATA-AGGAGCAGACACGATTACT
66 CGAGTCTTATACTCTCTGAACGAATAGAGG-GCAGACACGATTACT
* * * * * * * *
6382108 GAAGATTGTTCGAGT-TCTATACTCCCTGAAGGAATAGGGAGGAGACACGATTGTTGAAGATTAT
1 GAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTAAAAATCAG
* **
6382172 TCGAGTCTTATACTCTCTGAACGAATAGAGGGCAGACATGATTGTT
65 TCGAGTCTTATACTCTCTGAACGAATAGAGGGCAGACACGATTACT
* * * *
6382218 GAAGATTGTTCGAGTCTTACACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA-C-GT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTAAAAATCAG-
* *
6382281 TCGAGTTTTATACTCCCTGAA-GAA-AGAGGG
65 TCGAGTCTTATACTCTCTGAACGAATAGAGGG
6382311 AACAAACCCG
Statistics
Matches: 178, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
107 6 0.03
108 3 0.02
109 20 0.11
110 145 0.81
111 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTAAAAATCAGT
CGAGTCTTATACTCTCTGAACGAATAGAGGGCAGACACGATTACT
Found at i:6382190 original size:165 final size:164
Alignment explanation
Indices: 6381998--6382311 Score: 436
Period size: 165 Copynumber: 1.9 Consensus size: 164
6381988 CCTGTAGGAA
*
6381998 GAAGATTGTTCGAGTCTTATACTCTCTGAAAAAATAG-GGAGCAGACATGATTATTAAAAATCAG
1 GAAGATTATTCGAGTCTTATACTCTCTGAAAAAATAGAGG-GCAGACATGATTATTAAAAAT-AG
* *
6382062 -TCGAGTCTTATACTCTCTGAACG-AATAAGGAGCAGACACGATTACTGAAGATTGTTCGAGTTC
64 TTCGAGTCTTACACTCTCTGAA-GAAATAAGGAGCAGACACGATTACTGAAGA-CGTTCGAGTTC
* *
6382125 TATACTCCCTGAAGGAATAGGGAGGAGACACGATTGTT
127 TATACTCCCTGAAGAAAGAGGGAGGAGACACGATTGTT
** * * * *
6382163 GAAGATTATTCGAGTCTTATACTCTCTGAACGAATAGAGGGCAGACATGATTGTTGAAGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAAAAATAGAGGGCAGACATGATTATTAAAAATAGTT
* ** *
6382228 CGAGTCTTACACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGACGTTCGAGTTTTATA
66 CGAGTCTTACACTCTCTGAAGAAATAAGGAGCAGACACGATTACTGAAGACGTTCGAGTTCTATA
6382293 CTCCCTGAAGAAAGAGGGA
131 CTCCCTGAAGAAAGAGGGA
6382312 ACAAACCCGT
Statistics
Matches: 131, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
164 32 0.24
165 97 0.74
166 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (164 bp):
GAAGATTATTCGAGTCTTATACTCTCTGAAAAAATAGAGGGCAGACATGATTATTAAAAATAGTT
CGAGTCTTACACTCTCTGAAGAAATAAGGAGCAGACACGATTACTGAAGACGTTCGAGTTCTATA
CTCCCTGAAGAAAGAGGGAGGAGACACGATTGTT
Found at i:6388578 original size:90 final size:89
Alignment explanation
Indices: 6388423--6388589 Score: 298
Period size: 90 Copynumber: 1.9 Consensus size: 89
6388413 CCTAACACAC
*
6388423 CCTTTTATAGCCATGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
6388488 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATTAGAATTTAATAAT
* *
6388512 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATAT
6388577 ATTTAATTAATTA
65 ATTTAATTAATTA
6388590 AAACTAAATA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 33 0.45
90 41 0.55
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTAGAATTTAATAAT
Found at i:6390763 original size:22 final size:23
Alignment explanation
Indices: 6390738--6390781 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6390728 ATAAAAAATG
*
6390738 AAATAAGA-TAAAACAAAATAAA
1 AAATAAAATTAAAACAAAATAAA
*
6390760 AAATAAAATTAAAAGAAAATAA
1 AAATAAAATTAAAACAAAATAA
6390782 CATAAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (23 bp):
AAATAAAATTAAAACAAAATAAA
Found at i:6390897 original size:23 final size:23
Alignment explanation
Indices: 6390868--6390917 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
6390858 GGAGGAAAAT
*
6390868 AAAAAGTTAGGGAGTCAATTCGC
1 AAAAAGTTAGAGAGTCAATTCGC
6390891 AAAAAGTTAGAGAGTCAATTCGC
1 AAAAAGTTAGAGAGTCAATTCGC
6390914 AAAA
1 AAAA
6390918 TTTACAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (23 bp):
AAAAAGTTAGAGAGTCAATTCGC
Found at i:6391993 original size:5 final size:5
Alignment explanation
Indices: 6391975--6392230 Score: 73
Period size: 5 Copynumber: 51.2 Consensus size: 5
6391965 ACCTAAAATA
6391975 ATAAT -TAA- ATAAT ATAAT ATACA- ATAAT AATAACAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT -AT-A-AT ATAAT ATAAT
* * *
6392021 AATAAT A-ATAT ATAAT AGCAA- ATATAT ATATAT ATACT ATAAT AT-GT
1 -ATAAT ATA-AT ATAAT A-TAAT ATA-AT ATA-AT ATAAT ATAAT ATAAT
* *
6392068 A-ATAT ATAAT AT-A- ATAAT ATACT AT-AT GATTAT ATAA- ATAAT AT-AT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
* * ** *
6392114 A-ATAT ATAAT AT-AT AATAAT ATATT ATACT AT-AT ATTGT ATAA- ATACT
1 ATA-AT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * *
6392162 ATAAT AT-AT AATACCAT GTCAT ATAAT AT-AT ACT-GT ATAAA ATAATAT
1 ATAAT ATAAT -ATA--AT ATAAT ATAAT ATAAT A-TAAT ATAAT AT-A-AT
*
6392210 ATAAT ATAAT ATGAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT A
6392231 AAAAGGAATC
Statistics
Matches: 188, Mismatches: 27, Indels: 72
0.66 0.09 0.25
Matches are distributed among these distances:
3 2 0.01
4 35 0.19
5 111 0.59
6 29 0.15
7 7 0.04
8 4 0.02
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:6392037 original size:7 final size:7
Alignment explanation
Indices: 6391986--6392230 Score: 152
Period size: 7 Copynumber: 34.1 Consensus size: 7
6391976 TAATTAAATA
6391986 ATATAAT
1 ATATAAT
*
6391993 ATACAAT
1 ATATAAT
*
6392000 AATAATAAC
1 -AT-ATAAT
6392009 ATATAAT
1 ATATAAT
6392016 ATAATAAT
1 AT-ATAAT
6392024 A-ATAAT
1 ATATAAT
6392030 ATATAAT
1 ATATAAT
*
6392037 AGCA-AAT
1 A-TATAAT
6392044 ATAT-AT
1 ATATAAT
6392050 ATAT-AT
1 ATATAAT
6392056 ACTATAAT
1 A-TATAAT
*
6392064 ATGTAAT
1 ATATAAT
6392071 ATATAAT
1 ATATAAT
6392078 ATAATAAT
1 AT-ATAAT
6392086 ATACT-AT
1 ATA-TAAT
6392093 ATGATTATAT
1 AT-A-TA-AT
*
6392103 AAATAAT
1 ATATAAT
6392110 ATATAAT
1 ATATAAT
6392117 ATATAAT
1 ATATAAT
6392124 ATATAAT
1 ATATAAT
6392131 A-AT-AT
1 ATATAAT
*
6392136 ATTATACT
1 A-TATAAT
*
6392144 ATATATT
1 ATATAAT
*
6392151 GTATAAAT
1 ATAT-AAT
6392159 ACTATAAT
1 A-TATAAT
6392167 ATATAAT
1 ATATAAT
* *
6392174 ACCAT-GT
1 A-TATAAT
6392181 CATATAAT
1 -ATATAAT
*
6392189 ATATACT
1 ATATAAT
*
6392196 GTATAA-
1 ATATAAT
6392202 A-ATAAT
1 ATATAAT
6392208 ATATAAT
1 ATATAAT
6392215 ATA-ATAT
1 ATATA-AT
6392222 GATATAAT
1 -ATATAAT
6392230 A
1 A
6392231 AAAAGGAATC
Statistics
Matches: 188, Mismatches: 24, Indels: 52
0.71 0.09 0.20
Matches are distributed among these distances:
5 7 0.04
6 20 0.11
7 107 0.57
8 43 0.23
9 8 0.04
10 3 0.02
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:6392047 original size:2 final size:2
Alignment explanation
Indices: 6392042--6392171 Score: 81
Period size: 2 Copynumber: 69.5 Consensus size: 2
6392032 ATAATAGCAA
*
6392042 AT AT AT AT AT AT AT ACT AT A- AT AT GT A- AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6392081 AT A- AT AT ACT AT AT GAT -T AT AT AA AT A- AT AT AT A- AT AT AT
1 AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
6392121 A- AT AT AT A- AT A- AT AT AT -T AT ACT AT AT AT -T GT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
6392159 ACT AT A- AT AT AT A
1 A-T AT AT AT AT AT A
6392172 ATACCATGTC
Statistics
Matches: 102, Mismatches: 7, Indels: 38
0.69 0.05 0.26
Matches are distributed among these distances:
1 14 0.14
2 78 0.76
3 10 0.10
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:6392048 original size:53 final size:53
Alignment explanation
Indices: 6391971--6392174 Score: 164
Period size: 53 Copynumber: 3.9 Consensus size: 53
6391961 TTGGACCTAA
* *
6391971 AATAATAATTAA-ATA-ATAT-AATATA-CAATAATA-ATAACATATAATATAAT
1 AATAATAA-TAATATACATATGAATATATAAATAATATATAATATATAATAT-AT
* *
6392021 AATAATAAT-ATATA-ATA-GCAAATATATATATATATACTATAATATGTAATATAT
1 AATAATAATAATATACATATG--AATATATAAATA-ATA-TATAATATATAATATAT
*
6392075 AAT-ATAATAATATACTATATGATTATATAAATAATATATAATATATAATATAT
1 AATAATAATAATATAC-ATATGAATATATAAATAATATATAATATATAATATAT
* * * *
6392128 AATAAT-ATATTATACTATAT-ATTGTATAAAT-A-CTATAATATATAATA
1 AATAATAATAATATAC-ATATGAATATATAAATAATATATAATATATAATA
6392175 CCATGTCATA
Statistics
Matches: 131, Mismatches: 10, Indels: 26
0.78 0.06 0.16
Matches are distributed among these distances:
48 1 0.01
49 7 0.05
50 22 0.17
51 7 0.05
52 13 0.10
53 40 0.31
54 15 0.11
55 22 0.17
56 3 0.02
57 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (53 bp):
AATAATAATAATATACATATGAATATATAAATAATATATAATATATAATATAT
Found at i:6392063 original size:27 final size:32
Alignment explanation
Indices: 6391988--6392093 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 32
6391978 ATTAAATAAT
* *
6391988 ATAATATACAATAATAAT--AACATATAATATA
1 ATAATATACTATAAT-ATGCAATATATAATATA
*
6392019 ATAATAATAATAT-ATAATAGCAA-ATAT-ATAT-
1 ATAAT-ATACTATAAT-AT-GCAATATATAATATA
*
6392050 AT-ATATACTATAATATGTAATATATAATATA
1 ATAATATACTATAATATGCAATATATAATATA
6392081 ATAATATACTATA
1 ATAATATACTATA
6392094 TGATTATATA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
28 3 0.05
29 12 0.19
30 8 0.13
31 14 0.23
32 19 0.31
33 4 0.06
34 2 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (32 bp):
ATAATATACTATAATATGCAATATATAATATA
Found at i:6392094 original size:43 final size:42
Alignment explanation
Indices: 6391986--6392220 Score: 159
Period size: 41 Copynumber: 5.5 Consensus size: 42
6391976 TAATTAAATA
* *
6391986 ATATAATATA-CA-ATAATAATA-ACATATA-ATATAATAAT
1 ATATAATATATAATATAATAATATATATATATATATAATAAT
**
6392024 A-ATAATATATAATAGCA-AATATATATATATATACT-ATAAT
1 ATATAATATATAATATAATAATATATATATATATA-TAATAAT
*
6392064 ATGTAATATATAATATAATAATATACTATATGATTATATAAATAAT
1 ATATAATATATAATATAATAATATA-TATAT-A-TATAT-AATAAT
*
6392110 ATATAATATATAATATATAATAATATATTATACTATATATTGTATAAAT
1 ATATAATATAT-A-ATATAATAATATA-TATA-TATATA-T-AAT-AAT
** * *
6392159 ACTATAATATATAATACCAT-GTCATATA-ATATATACTGTATAA-
1 A-TATAATATATAATATAATAAT-ATATATATATATA-T-AATAAT
6392202 A-ATAATATATAATATAATA
1 ATATAATATATAATATAATA
6392221 TGATATAATA
Statistics
Matches: 160, Mismatches: 17, Indels: 36
0.75 0.08 0.17
Matches are distributed among these distances:
37 8 0.05
38 6 0.04
39 8 0.05
40 9 0.06
41 29 0.18
42 6 0.04
43 6 0.04
44 4 0.03
45 15 0.09
46 16 0.10
47 8 0.05
48 29 0.18
49 6 0.04
50 10 0.06
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (42 bp):
ATATAATATATAATATAATAATATATATATATATATAATAAT
Found at i:6398641 original size:13 final size:13
Alignment explanation
Indices: 6398623--6398666 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
6398613 ATAAATAATA
*
6398623 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
6398636 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
6398649 AAACAACTACAAT
1 AAAAAACTACAAT
6398662 AAAAA
1 AAAAA
6398667 GTACTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:6398800 original size:3 final size:3
Alignment explanation
Indices: 6398794--6398827 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
6398784 CTCCTCGTTG
* *
6398794 TCA TCA TCA TCA CCA TCA TCA TTA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
6398828 TGTCGTCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:6399184 original size:33 final size:33
Alignment explanation
Indices: 6399124--6399188 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
6399114 CTCCAGGAGG
* **
6399124 GGTCATATAACTCTGTGAAGGTAGCGGCGGCGA
1 GGTCATAAAACTAGGTGAAGGTAGCGGCGGCGA
* *
6399157 GGTCATAAAACTAGGTGATGGTGGCGGCGGCG
1 GGTCATAAAACTAGGTGAAGGTAGCGGCGGCG
6399189 GCATCAGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (33 bp):
GGTCATAAAACTAGGTGAAGGTAGCGGCGGCGA
Found at i:6400944 original size:7 final size:7
Alignment explanation
Indices: 6400932--6400979 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
6400922 AAAAATTAAG
6400932 TAAATAT
1 TAAATAT
6400939 TAAATAT
1 TAAATAT
*
6400946 TAAAAACT
1 TAAATA-T
6400954 TAAATAAT
1 TAAAT-AT
*
6400962 TAAATAC
1 TAAATAT
*
6400969 AAAATAT
1 TAAATAT
6400976 TAAA
1 TAAA
6400980 ATATAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 21 0.64
8 11 0.33
9 1 0.03
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (7 bp):
TAAATAT
Found at i:6400958 original size:15 final size:15
Alignment explanation
Indices: 6400938--6400980 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6400928 TAAGTAAATA
6400938 TTAAATATTAAAAAC
1 TTAAATATTAAAAAC
*
6400953 TTAAATAATTAAATAC
1 TTAAAT-ATTAAAAAC
*
6400969 -AAAATATTAAAA
1 TTAAATATTAAAA
6400981 TATAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 10 0.42
16 8 0.33
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAATATTAAAAAC
Found at i:6404114 original size:74 final size:74
Alignment explanation
Indices: 6403993--6404143 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
6403983 GGCTTAGCTT
*
6403993 TTGACATAAATGTCATAATGGTAGGTGTTATTTTCCCTGAAATCTAGCCTTTATAACGGTTGAAC
1 TTGACATAAATGTCATAATGGTAGGTATTATTTTCCCTGAAATCTAGCCTTTATAACGGTTGAAC
6404058 ATAAAAATG
66 ATAAAAATG
6404067 TTGACATAAATGTCATAATGGTAGGTATTATTTTCCCTGAAATCTAGCCTTTATAACGGTTGAAC
1 TTGACATAAATGTCATAATGGTAGGTATTATTTTCCCTGAAATCTAGCCTTTATAACGGTTGAAC
6404132 ATAAAAATG
66 ATAAAAATG
6404141 TTG
1 TTG
6404144 TATATATATA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (74 bp):
TTGACATAAATGTCATAATGGTAGGTATTATTTTCCCTGAAATCTAGCCTTTATAACGGTTGAAC
ATAAAAATG
Found at i:6404616 original size:60 final size:58
Alignment explanation
Indices: 6404492--6404625 Score: 135
Period size: 60 Copynumber: 2.3 Consensus size: 58
6404482 AAATACGATC
* * ** * *
6404492 TCATTCTAAACTGGTCTTAAAATTTTAAAATTTTAATTTTATATCCAAATCATGACTC
1 TCATTCTAAACTAGTCTTAAAATTTGAAAATTACAATTTCATATCCAAATCATGACTA
* * * *
6404550 TAATTCTAACCTAGTCTTTAAAATATTGAATATTACAATTTCATATCCAAA-CTATGATTA
1 TCATTCTAAACTAGTC-TTAAAAT-TTGAAAATTACAATTTCATATCCAAATC-ATGACTA
*
6404610 TCATTCTAAATTAGTC
1 TCATTCTAAACTAGTC
6404626 CCGAAACTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
58 13 0.22
59 8 0.13
60 39 0.65
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (58 bp):
TCATTCTAAACTAGTCTTAAAATTTGAAAATTACAATTTCATATCCAAATCATGACTA
Found at i:6404919 original size:39 final size:39
Alignment explanation
Indices: 6404859--6404964 Score: 167
Period size: 39 Copynumber: 2.7 Consensus size: 39
6404849 TTAAAATGTC
* *
6404859 CAAAAGTTTAAGAACTCATTTAAAATGATGGTCAACATT
1 CAAAAGTTTAAGGACTAATTTAAAATGATGGTCAACATT
*
6404898 CAAAAGTTTAAGGACTAATTTAAAATGATGGTCAATATT
1 CAAAAGTTTAAGGACTAATTTAAAATGATGGTCAACATT
* *
6404937 TAAAAGTTTAAGGACTAACTTAAAATGA
1 CAAAAGTTTAAGGACTAATTTAAAATGA
6404965 AAATCATAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.31
Consensus pattern (39 bp):
CAAAAGTTTAAGGACTAATTTAAAATGATGGTCAACATT
Found at i:6404977 original size:39 final size:39
Alignment explanation
Indices: 6404860--6404978 Score: 114
Period size: 39 Copynumber: 3.1 Consensus size: 39
6404850 TAAAATGTCC
* * * *** * *
6404860 AAAAGTTTAAGAACTCATTTAAAATGATGGTCAACATTC
1 AAAAGTTTAAGGACTAACTTAAAATGAAAATCAATATTT
* ***
6404899 AAAAGTTTAAGGACTAATTTAAAATGATGGTCAATATTT
1 AAAAGTTTAAGGACTAACTTAAAATGAAAATCAATATTT
6404938 AAAAGTTTAAGGACTAACTTAAAATGAAAATC-ATAATTT
1 AAAAGTTTAAGGACTAACTTAAAATGAAAATCAAT-ATTT
6404977 AA
1 AA
6404979 TGATGTGCGA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 2 0.03
39 69 0.97
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (39 bp):
AAAAGTTTAAGGACTAACTTAAAATGAAAATCAATATTT
Found at i:6405483 original size:25 final size:25
Alignment explanation
Indices: 6405453--6405528 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
6405443 CAACTAACTT
6405453 TATTATTTATTGATTAATCTTCAAA
1 TATTATTTATTGATTAATCTTCAAA
* ** * *
6405478 TGTTATACATGGATT-A-C-TAAAA
1 TATTATTTATTGATTAATCTTCAAA
6405500 TTATTATTTATTGATTAATCTTCAAA
1 -TATTATTTATTGATTAATCTTCAAA
6405526 TAT
1 TAT
6405529 CACGTGCTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 2 0.05
25 15 0.41
26 4 0.11
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.49
Consensus pattern (25 bp):
TATTATTTATTGATTAATCTTCAAA
Found at i:6405548 original size:48 final size:46
Alignment explanation
Indices: 6405452--6405548 Score: 106
Period size: 48 Copynumber: 2.0 Consensus size: 46
6405442 CCAACTAACT
* * *
6405452 TTATTATTTATTGATTAATCTTCAAATGTTATACATGGATTACTAAAA
1 TTATTATTTATTGATTAATCTTCAAA--TTATACATGAATCACCAAAA
*
6405500 TTATTATTTATTGATTAATCTTCAAA-TATCACGTGCTAATCACCAAAA
1 TTATTATTTATTGATTAATCTTCAAATTAT-ACATG--AATCACCAAAA
6405548 T
1 T
6405549 GTTACTTGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
45 3 0.07
46 4 0.10
48 35 0.83
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (46 bp):
TTATTATTTATTGATTAATCTTCAAATTATACATGAATCACCAAAA
Found at i:6409758 original size:17 final size:17
Alignment explanation
Indices: 6409736--6409769 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6409726 GGAGTTGGTT
*
6409736 GGGGTTGGTTTGTAATA
1 GGGGTTGCTTTGTAATA
*
6409753 GGGGTTTCTTTGTAATA
1 GGGGTTGCTTTGTAATA
6409770 AAAAAATGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (17 bp):
GGGGTTGCTTTGTAATA
Found at i:6410602 original size:21 final size:22
Alignment explanation
Indices: 6410578--6410621 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6410568 ATTAATTTAT
6410578 TATT-ATGATAATTTTAAAATA
1 TATTAATGATAATTTTAAAATA
* **
6410599 TATTAATTATGCTTTTAAAATA
1 TATTAATGATAATTTTAAAATA
6410621 T
1 T
6410622 TATTTTAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTAATGATAATTTTAAAATA
Found at i:6411555 original size:20 final size:20
Alignment explanation
Indices: 6411530--6411576 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
6411520 ATTAAGTAAG
*
6411530 GGTGAATGCTAAGCTTTGGT
1 GGTGAATACTAAGCTTTGGT
6411550 GGTGAATACTAAGCTTTGGT
1 GGTGAATACTAAGCTTTGGT
6411570 GGTGAAT
1 GGTGAAT
6411577 TTTATTCGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.34, T:0.34
Consensus pattern (20 bp):
GGTGAATACTAAGCTTTGGT
Found at i:6415647 original size:18 final size:19
Alignment explanation
Indices: 6415610--6415647 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6415600 TGAAAATGAT
*
6415610 TTGATTTTGAAAGCAAAAA
1 TTGATTTTGAAAGAAAAAA
6415629 TTGATTTTGAAA-AAAAAA
1 TTGATTTTGAAAGAAAAAA
6415647 T
1 T
6415648 GAAACTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (19 bp):
TTGATTTTGAAAGAAAAAA
Found at i:6417184 original size:20 final size:20
Alignment explanation
Indices: 6417159--6417210 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
6417149 CTTTACATAG
*
6417159 TAGTATCAATACCATAGGCT
1 TAGTATCGATACCATAGGCT
6417179 TAGTATCGATACCATAGGCT
1 TAGTATCGATACCATAGGCT
6417199 TAGTATCGATAC
1 TAGTATCGATAC
6417211 TTTCAGACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (20 bp):
TAGTATCGATACCATAGGCT
Found at i:6418159 original size:16 final size:16
Alignment explanation
Indices: 6418139--6418177 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6418129 AGAGAGCAAT
6418139 AAGAAAA-GAGAAAAGA
1 AAGAAAAGGA-AAAAGA
*
6418155 TAGAAAAGGAAAAAGA
1 AAGAAAAGGAAAAAGA
6418171 AAGAAAA
1 AAGAAAA
6418178 ATAGAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (16 bp):
AAGAAAAGGAAAAAGA
Found at i:6418183 original size:24 final size:25
Alignment explanation
Indices: 6418139--6418225 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 25
6418129 AGAGAGCAAT
*
6418139 AAGAA-AAGAGAAAAGATAGAAAAGGA
1 AAGAAGAA-AGAAAA-ATAGAAAAGAA
*
6418165 AA-AAGAAAGAAAAATAGAAAAAGTA
1 AAGAAGAAAGAAAAATAG-AAAAGAA
* * * *
6418190 AATAAAAAATAAAAAGAG-AAAGAA
1 AAGAAGAAAGAAAAATAGAAAAGAA
6418214 AAGAAGAAAGAA
1 AAGAAGAAAGAA
6418226 GAAAAAACAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
24 18 0.36
25 16 0.32
26 16 0.32
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (25 bp):
AAGAAGAAAGAAAAATAGAAAAGAA
Found at i:6418203 original size:26 final size:25
Alignment explanation
Indices: 6418142--6418210 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
6418132 GAGCAATAAG
*
6418142 AAAAGAGAAAAGATAG-AAAAGGAAA
1 AAAAAAGAAAA-ATAGAAAAAGGAAA
* *
6418167 AAGAAAGAAAAATAGAAAAAGTAAA
1 AAAAAAGAAAAATAGAAAAAGGAAA
* *
6418192 TAAAAAATAAAAAGAGAAA
1 -AAAAAAGAAAAATAGAAA
6418211 GAAAAGAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 4 0.11
25 17 0.47
26 15 0.42
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (25 bp):
AAAAAAGAAAAATAGAAAAAGGAAA
Found at i:6418215 original size:19 final size:19
Alignment explanation
Indices: 6418163--6418229 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
6418153 GATAGAAAAG
6418163 GAAAAAGAAAG-AAAAATA
1 GAAAAAGAAAGAAAAAATA
*
6418181 GAAAAAGTAAATAAAAAATA
1 GAAAAAG-AAAGAAAAAATA
*
6418201 -AAAAGAGAAAGAAAAGA-A
1 GAAAA-AGAAAGAAAAAATA
6418219 GAAAGAAGAAA
1 GAAA-AAGAAA
6418230 AAACATATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 8 0.20
19 23 0.56
20 10 0.24
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (19 bp):
GAAAAAGAAAGAAAAAATA
Found at i:6419971 original size:79 final size:79
Alignment explanation
Indices: 6419872--6420373 Score: 528
Period size: 79 Copynumber: 6.3 Consensus size: 79
6419862 CGATTAGGGA
* * *
6419872 GAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTGTTCGATTCCATCATAGAAGGAGGTGGA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGGTGGA
6419937 TCAACATTTCCAAT
66 TCAACATTTCCAAT
* * ** * *
6419951 G-AGTAAGTTCATAATCAGAAGAAGTTGTTCAATTTTTGCT-GAAATCCATCACAGAAGAAGGTG
1 GAAG-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCG-ATTCCATCACAGAAGGAGGTG
*
6420014 GATCAACATTTCCAGT
64 GATCAACATTTCCAAT
* * * * * *
6420030 GAAGAATTTCATAATGAGAAGAACTTGTTTAACCTTTACTCGATTACATCACAAAAGGAGGTGTA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGGTGGA
*
6420095 TCATCATTTCCAAT
66 TCAACATTTCCAAT
* * * * * * *
6420109 GAAGAAGTTCATAGTGACAAGAACTTCTTCAACCTTTACTCAATTCCATCATAGAAGGAGGTAGA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGGTGGA
6420174 TCAACATTTCCAAT
66 TCAACATTTCCAAT
* * ** * *
6420188 G-AGTAAGTTCATAATCAGAAGAAGTTGTTCAATTTTTGCT-GAAATCCATCACAGAAGAAGGTG
1 GAAG-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCG-ATTCCATCACAGAAGGAGGTG
*
6420251 GATCAACATTTCCAGT
64 GATCAACATTTCCAAT
* * * ** * * *
6420267 GAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTT-TTCCGATTGCATCATGGAATGAGTTAG
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCT-CGATTCCATCACAGAAGGAGGTGG
* *
6420331 ATCAACATTCCCAAA
65 ATCAACATTTCCAAT
* *
6420346 AAGAGAAGTTCGTAATGAGAAGAACTTG
1 GA-AGAAGTTCATAATGAGAAGAACTTG
6420374 CAAAAATATT
Statistics
Matches: 344, Mismatches: 69, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
78 6 0.02
79 308 0.90
80 30 0.09
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (79 bp):
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGGTGGA
TCAACATTTCCAAT
Found at i:6420287 original size:237 final size:237
Alignment explanation
Indices: 6419872--6420303 Score: 765
Period size: 237 Copynumber: 1.8 Consensus size: 237
6419862 CGATTAGGGA
* * * ** * *
6419872 GAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTGTTCGATTCCATCATAGAAGGAGGTGGA
1 GAAGAAGTTCATAATGACAAGAACTTCTTCAACCTTTACTCAATTCCATCATAGAAGGAGGTAGA
6419937 TCAACATTTCCAATGAGTAAGTTCATAATCAGAAGAAGTTGTTCAATTTTTGCTGAAATCCATCA
66 TCAACATTTCCAATGAGTAAGTTCATAATCAGAAGAAGTTGTTCAATTTTTGCTGAAATCCATCA
* * *
6420002 CAGAAGAAGGTGGATCAACATTTCCAGTGAAGAATTTCATAATGAGAAGAACTTGTTTAACCTTT
131 CAGAAGAAGGTGGATCAACATTTCCAGTGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTT
6420067 ACTCGATTACATCACAAAAGGAGGTGTATCATCATTTCCAAT
196 ACTCGATTACATCACAAAAGGAGGTGTATCATCATTTCCAAT
*
6420109 GAAGAAGTTCATAGTGACAAGAACTTCTTCAACCTTTACTCAATTCCATCATAGAAGGAGGTAGA
1 GAAGAAGTTCATAATGACAAGAACTTCTTCAACCTTTACTCAATTCCATCATAGAAGGAGGTAGA
6420174 TCAACATTTCCAATGAGTAAGTTCATAATCAGAAGAAGTTGTTCAATTTTTGCTGAAATCCATCA
66 TCAACATTTCCAATGAGTAAGTTCATAATCAGAAGAAGTTGTTCAATTTTTGCTGAAATCCATCA
6420239 CAGAAGAAGGTGGATCAACATTTCCAGTGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTT
131 CAGAAGAAGGTGGATCAACATTTCCAGTGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTT
6420304 TTCCGATTGC
Statistics
Matches: 184, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
237 184 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (237 bp):
GAAGAAGTTCATAATGACAAGAACTTCTTCAACCTTTACTCAATTCCATCATAGAAGGAGGTAGA
TCAACATTTCCAATGAGTAAGTTCATAATCAGAAGAAGTTGTTCAATTTTTGCTGAAATCCATCA
CAGAAGAAGGTGGATCAACATTTCCAGTGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTT
ACTCGATTACATCACAAAAGGAGGTGTATCATCATTTCCAAT
Found at i:6420896 original size:3 final size:3
Alignment explanation
Indices: 6420890--6420935 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
6420880 GTTGTTGTTG
*
6420890 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6420936 ACAAGCCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6421775 original size:23 final size:21
Alignment explanation
Indices: 6421742--6421805 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
6421732 TTTTGATCAC
6421742 TTTGATTTTATCCCATATTTAT
1 TTTG-TTTTATCCCATATTTAT
**
6421764 TTTGGTTCTTATTTCAT-TTTAT
1 TTT-GTT-TTATCCCATATTTAT
6421786 TTTGTTTTAGTCCCTATATT
1 TTTGTTTTA-TCCC-ATATT
6421806 ATTGCGTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 15 0.45
23 10 0.30
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.62
Consensus pattern (21 bp):
TTTGTTTTATCCCATATTTAT
Found at i:6424652 original size:27 final size:27
Alignment explanation
Indices: 6424597--6424662 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
6424587 TAATTTGAAA
6424597 AATAAATTATTAATTATAATAATTAGATT
1 AATAAA-T-TTAATTATAATAATTAGATT
* * *
6424626 AATAAATTTAATTATGATCATTGGATT
1 AATAAATTTAATTATAATAATTAGATT
6424653 AATAAATTTA
1 AATAAATTTA
6424663 CTATCTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 27 0.79
28 1 0.03
29 6 0.18
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (27 bp):
AATAAATTTAATTATAATAATTAGATT
Found at i:6424656 original size:39 final size:38
Alignment explanation
Indices: 6424613--6424696 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 38
6424603 TTATTAATTA
* *
6424613 TAATAATTAGATTAATAAAT-TTAATTATGATCATTGGAT
1 TAATAATT-GACT-ATAAATATTAATTATGATCATTAGAT
* **
6424652 TAATAAATTTACTATCTATATTAATTATGATCATTAGAT
1 TAAT-AATTGACTATAAATATTAATTATGATCATTAGAT
6424691 TAATAA
1 TAATAA
6424697 ATTTAATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
38 6 0.16
39 28 0.74
40 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (38 bp):
TAATAATTGACTATAAATATTAATTATGATCATTAGAT
Found at i:6424697 original size:39 final size:39
Alignment explanation
Indices: 6424633--6424726 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
6424623 ATTAATAAAT
* *
6424633 TTAATTATGATCATTGGATTAATAAATTTACTATCTATA
1 TTAATTATGATCATTAGATTAATAAATTTAATATCTATA
*
6424672 TTAATTATGATCATTAGATTAATAAATTTAATTTCTATA
1 TTAATTATGATCATTAGATTAATAAATTTAATATCTATA
* *
6424711 CTAATTATGATTATTA
1 TTAATTATGATCATTA
6424727 TGTTAGAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (39 bp):
TTAATTATGATCATTAGATTAATAAATTTAATATCTATA
Found at i:6425147 original size:29 final size:31
Alignment explanation
Indices: 6425080--6425147 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
6425070 TATTCAACAG
6425080 TTTAATTAAATTAATAATTTATGATTGATAAA
1 TTTAATTAAA-TAATAATTTATGATTGATAAA
* *
6425112 TAT-ATTAAA-AATAA-TTATTGATT-ATAAC
1 TTTAATTAAATAATAATTTA-TGATTGATAAA
6425140 TTTAATTA
1 TTTAATTA
6425148 TGATTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
28 9 0.29
29 14 0.45
31 6 0.19
32 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (31 bp):
TTTAATTAAATAATAATTTATGATTGATAAA
Found at i:6425319 original size:30 final size:29
Alignment explanation
Indices: 6425266--6425337 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 29
6425256 TTTATTTAAG
*
6425266 TACCTAAAGTATTTTTTGGTC-AAATAAA
1 TACCTAAAGTATTTTTTGATCAAAATAAA
**
6425294 TACCTAAACGTATCTTTTTGATCAAAATAGG
1 TACCTAAA-GTAT-TTTTTGATCAAAATAAA
6425325 TACCTAAAGTATT
1 TACCTAAAGTATT
6425338 CATTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 8 0.21
29 5 0.13
30 12 0.32
31 13 0.34
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (29 bp):
TACCTAAAGTATTTTTTGATCAAAATAAA
Done.