Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 11 of 22
Found at i:5623141 original size:46 final size:46
Alignment explanation
Indices: 5623074--5623165 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
5623064 CTTTTAATCT
5623074 CTCACCCTCAAGCTTCACAAAGTC-GACAATCCTATAATCTCTCACC
1 CTCACCCTCAAGCTTCACAAAGTCAG-CAATCCTATAATCTCTCACC
* *
5623120 CTCACCCTCTAGCTTCACAAAGTCAGCGATCCTATAATCTCTCACC
1 CTCACCCTCAAGCTTCACAAAGTCAGCAATCCTATAATCTCTCACC
5623166 TTTAAGCCNN
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 42 0.98
47 1 0.02
ACGTcount: A:0.28, C:0.39, G:0.08, T:0.25
Consensus pattern (46 bp):
CTCACCCTCAAGCTTCACAAAGTCAGCAATCCTATAATCTCTCACC
Found at i:5632171 original size:169 final size:167
Alignment explanation
Indices: 5631866--5632238 Score: 538
Period size: 169 Copynumber: 2.2 Consensus size: 167
5631856 TTACAAAAAC
* * *
5631866 AAATTATATTGTAGGACACCGCTACTCTATCTTAACCTTACATAACCTTCATTAATTTGTATTTT
1 AAATTATATTGTAGGACACTGCTACTCTATCTTAACCTTACATAACCTTCAATAATTTGTATTTC
* * *
5631931 CTGGAGGAGATCCATAAATTTATTTTTGTCCTTAGATTAATATGTATGTAGCATGTACATAAATT
66 CTGGAGCAGATCCATAAATTTATTTTTGTCCTTAGATTAATATGCATGTAGCATGTACATAAATA
*
5631996 TTACTAGAAATGTCACTAGCTTTGATTTTGCGAAAA-G
131 TTACTAGAAATGTCACTAACTTTGATTTTGC-AAAAGG
* * *
5632033 AAGTTATATTGTAGGACACTGCTACTCTATCTTAACCTTATATAAGCTT-AATAATTTGTATTTC
1 AAATTATATTGTAGGACACTGCTACTCTATCTTAACCTTACATAACCTTCAATAATTTGTATTTC
*
5632097 CTGG-GCA-ATCCATAAATTTATCTCAGTTTTGTCCTTAGATTAATATGCCTGTAGCATGTACAT
66 CTGGAGCAGATCCATAAATTTA--T---TTTTGTCCTTAGATTAATATGCATGTAGCATGTACAT
*
5632160 AAATATTACTAGAAATGTCACTAATTTTGATTTTGCAAAAGG
126 AAATATTACTAGAAATGTCACTAACTTTGATTTTGCAAAAGG
* *
5632202 AAATTACATTGTAGGACACTGCTACCCTATCTTAACC
1 AAATTATATTGTAGGACACTGCTACTCTATCTTAACC
5632239 AGACAGAAAC
Statistics
Matches: 185, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
164 13 0.07
165 2 0.01
166 18 0.10
167 45 0.24
168 4 0.02
169 103 0.56
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (167 bp):
AAATTATATTGTAGGACACTGCTACTCTATCTTAACCTTACATAACCTTCAATAATTTGTATTTC
CTGGAGCAGATCCATAAATTTATTTTTGTCCTTAGATTAATATGCATGTAGCATGTACATAAATA
TTACTAGAAATGTCACTAACTTTGATTTTGCAAAAGG
Found at i:5637798 original size:18 final size:17
Alignment explanation
Indices: 5637764--5637847 Score: 72
Period size: 18 Copynumber: 5.0 Consensus size: 17
5637754 GGATTTAGTT
5637764 ATTTT-TCTAATTAATTTA
1 ATTTTATCT-ATT-ATTTA
5637782 ATTTTATCTAGTTATTTA
1 ATTTTATCTA-TTATTTA
5637800 ATTTTATGCTATT-TTTA
1 ATTTTAT-CTATTATTTA
5637817 ATTTT-T-T-TTACTTTA
1 ATTTTATCTATTA-TTTA
*
5637832 ATTTAAT-TATTATTTA
1 ATTTTATCTATTATTTA
5637848 TTAATTTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
13 2 0.03
14 1 0.02
15 8 0.14
16 7 0.12
17 12 0.21
18 20 0.34
19 8 0.14
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTTTATCTATTATTTA
Found at i:5639215 original size:18 final size:16
Alignment explanation
Indices: 5639179--5639225 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
5639169 TATCGACACT
5639179 TTATTTA-TTAATATA
1 TTATTTATTTAATATA
5639194 TTATTTATTTAATATGTA
1 TTATTTATTTAATA--TA
*
5639212 TTATTTATTCAATA
1 TTATTTATTTAATA
5639226 CGGGTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 7 0.25
16 6 0.21
18 15 0.54
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TTATTTATTTAATATA
Found at i:5648359 original size:22 final size:22
Alignment explanation
Indices: 5648317--5648359 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5648307 ACTAATTAGG
* *
5648317 TATTTGAAATAGCTATTTCAAA
1 TATTTGAAATACCTATCTCAAA
5648339 TATTT-AAATACCTAATCTCAA
1 TATTTGAAATACCT-ATCTCAA
5648360 CAAAATCCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (22 bp):
TATTTGAAATACCTATCTCAAA
Found at i:5656852 original size:2 final size:2
Alignment explanation
Indices: 5656836--5656870 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5656826 TTCTGGTCAA
5656836 TC TC -C TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5656871 TTGCGTGCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:5657960 original size:2 final size:2
Alignment explanation
Indices: 5657955--5658024 Score: 59
Period size: 2 Copynumber: 35.0 Consensus size: 2
5657945 ACATATATGC
* * * * *
5657955 AT AT AT AT TT AT AT AT AT AT TT AT AT AT GT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
5657997 AT GT AT AT AT GT GT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5658025 GTGTGTGTAT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (2 bp):
AT
Found at i:5657962 original size:10 final size:10
Alignment explanation
Indices: 5657947--5658054 Score: 84
Period size: 10 Copynumber: 11.4 Consensus size: 10
5657937 ACATGCATAC
*
5657947 ATATATGCAT
1 ATATATGTAT
5657957 ATATAT-T-T
1 ATATATGTAT
5657965 ATATA--TAT
1 ATATATGTAT
* *
5657973 ATTTATATAT
1 ATATATGTAT
* *
5657983 GTGTATGTAT
1 ATATATGTAT
5657993 ATATATGTAT
1 ATATATGTAT
*
5658003 ATATGTGTAT
1 ATATATGTAT
5658013 ATATAT-T-T
1 ATATATGTAT
* *
5658021 ATATGTGTGT
1 ATATATGTAT
*
5658031 GTATATGTAT
1 ATATATGTAT
*
5658041 GTATATGTAT
1 ATATATGTAT
5658051 ATAT
1 ATAT
5658055 GTAAGTGTGT
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
7 1 0.01
8 17 0.22
9 2 0.03
10 59 0.75
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (10 bp):
ATATATGTAT
Found at i:5658003 original size:6 final size:6
Alignment explanation
Indices: 5657978--5658052 Score: 55
Period size: 6 Copynumber: 12.8 Consensus size: 6
5657968 TATATATTTA
* * * * * * *
5657978 TATATG TGTATG TATATA TATGTA TATATG TGTATA TATATT TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* *
5658026 TGTGTG TATATG --TATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATAT
5658053 ATGTAAGTGT
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
4 4 0.08
6 48 0.92
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:5658031 original size:22 final size:22
Alignment explanation
Indices: 5657968--5658048 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
5657958 TATATTTATA
* * *
5657968 TATATATTTATATATGTGTATG
1 TATATATATGTATATGTGTGTG
*
5657990 TATATATATGTATA--TATGTG
1 TATATATATGTATATGTGTGTG
*
5658010 TATATATATTTATATGTGTGTG
1 TATATATATGTATATGTGTGTG
*
5658032 TATATGTATGTATATGT
1 TATATATATGTATATGT
5658049 ATATATGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.35
22 32 0.65
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (22 bp):
TATATATATGTATATGTGTGTG
Found at i:5658057 original size:18 final size:18
Alignment explanation
Indices: 5657947--5658054 Score: 81
Period size: 18 Copynumber: 5.8 Consensus size: 18
5657937 ACATGCATAC
* *
5657947 ATATATGCATATATATTT
1 ATATATGTATATATATGT
* * *
5657965 ATATATATATTTATATAT
1 ATATATGTATATATATGT
* *
5657983 GTGTATGTATATATATGT
1 ATATATGTATATATATGT
*
5658001 ATATATGTGTATATATATTT
1 ATATA--TGTATATATATGT
* * *
5658021 ATATGTGTGTGTATATGT
1 ATATATGTATATATATGT
5658039 ATGTATATGTATATAT
1 A--TATATGTATATAT
5658055 GTAAGTGTGT
Statistics
Matches: 67, Mismatches: 19, Indels: 6
0.73 0.21 0.07
Matches are distributed among these distances:
18 41 0.61
20 26 0.39
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (18 bp):
ATATATGTATATATATGT
Found at i:5658861 original size:2 final size:2
Alignment explanation
Indices: 5658854--5658879 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5658844 GTAGTTTTCA
5658854 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5658880 TCATTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5671169 original size:2 final size:2
Alignment explanation
Indices: 5671162--5671203 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5671152 TCATATTCGT
5671162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5671204 CGTTGTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5672802 original size:11 final size:11
Alignment explanation
Indices: 5672759--5672783 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5672749 TAGTGTAGGG
5672759 GAAATTTGACA
1 GAAATTTGACA
5672770 GAAATTTGACA
1 GAAATTTGACA
5672781 GAA
1 GAA
5672784 CATTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (11 bp):
GAAATTTGACA
Found at i:5674490 original size:6 final size:7
Alignment explanation
Indices: 5674475--5674499 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5674465 CTCATAACTT
5674475 AAAATAA
1 AAAATAA
5674482 AAAATAA
1 AAAATAA
5674489 AAAATAA
1 AAAATAA
5674496 AAAA
1 AAAA
5674500 AATATTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:5690984 original size:28 final size:28
Alignment explanation
Indices: 5690953--5691011 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
5690943 AATTTGAAAT
5690953 TTTATTTATATTTGATGTAATGTATTTG
1 TTTATTTATATTTGATGTAATGTATTTG
* *
5690981 TTTATTTATTTTTGATGTAATTTATTTG
1 TTTATTTATATTTGATGTAATGTATTTG
5691009 TTT
1 TTT
5691012 GTAATATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (28 bp):
TTTATTTATATTTGATGTAATGTATTTG
Found at i:5691451 original size:14 final size:14
Alignment explanation
Indices: 5691402--5691452 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
5691392 CTTCCTCTCA
5691402 TCCT-TTCTTTTTC
1 TCCTCTTCTTTTTC
5691415 TCCTCTT-TTTTATC
1 TCCTCTTCTTTT-TC
* * *
5691429 TCTTATTCTCTTTC
1 TCCTCTTCTTTTTC
5691443 TCCTCTTCTT
1 TCCTCTTCTT
5691453 CTTCCACTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 8 0.28
14 18 0.62
15 3 0.10
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (14 bp):
TCCTCTTCTTTTTC
Found at i:5698602 original size:284 final size:277
Alignment explanation
Indices: 5698047--5698607 Score: 752
Period size: 284 Copynumber: 2.0 Consensus size: 277
5698037 TTTTTTTGTT
* *
5698047 TATTAAGGCATATTTTCCCTTTTACACTGCTGTTTTTCCTTTAGGAAAACGAAATTCTTACTTTT
1 TATTAAGACATATTTTCCCTTTTACACTGCTGTTTTTCCTTCAGGAAAACGAAATTCTTACTTTT
* * *
5698112 ACTAAGAGCTCTGTAGTGCCAATTACCATGTGACTCTTTAGTCTCCTAAAGTTTCCTTCAGAATG
66 ACTAAGAGCTCTGTAGTGCCAATTACCATGTGACTCGTCAGTCTCCTAAAGTTTCCTTCAGAATA
* * *
5698177 AGGAGCTGGAAAATAAGGAAGCCTTTGACTTTATCTTGGTCTCTTCATCTTTAGGGTTCATTTAA
131 AGGAGCTGGAAAATAAGGAACCCTTTGACTTTATCTTGGCCTCTTCAACTTTAGGGTTCATTTAA
** * *
5698242 GCCTGCTCATAGGTGTTTTCTTATGTGAACTGGGTTGATAATAAAAATGGTTGTTGGTGTTTCAA
196 GCCTGCTCATAGGCATTTACTTATGTGAACTGGCTTGATAATAAAAATGGTTGTTGGTGTTTCAA
5698307 TGGCTTGTCTCTGACAA
261 TGGCTTGTCTCTGACAA
* * *
5698324 TATTAAGACATATTTT-CTTTTTAACACTGCTG-TTTTCCTTCAGGAAAATGAAATTCTTTCTTT
1 TATTAAGACATATTTTCCCTTTT-ACACTGCTGTTTTTCCTTCAGGAAAACGAAATTCTTACTTT
* * * *
5698387 TACTAAGAGCTCTGTAGTGTCAATTACTATGTGACTCGTCAGTCTGCTAAA-TTTTCTTCAGAAT
65 TACTAAGAGCTCTGTAGTGCCAATTACCATGTGACTCGTCAGTCTCCTAAAGTTTCCTTCAGAAT
* * ** *
5698451 AAGGAGCTGGTAATTAAGTTTGCCCCCTTACTTTTG-TTCTTATCTTGGCCTCTTCAACTTTAGG
130 AAGGAGCTGGAAAATAAG---G-AACC---C-TTTGACT-TTATCTTGGCCTCTTCAACTTTAGG
* *
5698515 GTTCATTTTAGGCCTGCTCATAGGCATTTACTTATGTGCACTGGCTTGATAATAAAAATGGTTGT
186 GTTCA-TTTAAGCCTGCTCATAGGCATTTACTTATGTGAACTGGCTTGATAATAAAAATGGTTGT
*
5698580 TGGTGTTTCAATGTCTTGTCTCTGACAA
250 TGGTGTTTCAATGGCTTGTCTCTGACAA
5698608 GCATTGTGCC
Statistics
Matches: 246, Mismatches: 27, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
275 27 0.11
276 79 0.32
277 24 0.10
278 1 0.00
279 1 0.00
282 2 0.01
283 32 0.13
284 80 0.33
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (277 bp):
TATTAAGACATATTTTCCCTTTTACACTGCTGTTTTTCCTTCAGGAAAACGAAATTCTTACTTTT
ACTAAGAGCTCTGTAGTGCCAATTACCATGTGACTCGTCAGTCTCCTAAAGTTTCCTTCAGAATA
AGGAGCTGGAAAATAAGGAACCCTTTGACTTTATCTTGGCCTCTTCAACTTTAGGGTTCATTTAA
GCCTGCTCATAGGCATTTACTTATGTGAACTGGCTTGATAATAAAAATGGTTGTTGGTGTTTCAA
TGGCTTGTCTCTGACAA
Found at i:5710393 original size:30 final size:29
Alignment explanation
Indices: 5710357--5710433 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 29
5710347 AATAGTTAAT
**
5710357 TATAAAAATTTATTTGATTTAAAATAAAAA
1 TATAAAAATTTATTT-AAATAAAATAAAAA
* *
5710387 TATAAAAATTTAATTAAATATAATAAAAA
1 TATAAAAATTTATTTAAATAAAATAAAAA
5710416 -ATAAAAATTTATTTAAAT
1 TATAAAAATTTATTTAAAT
5710434 TTTTTGTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 17 0.40
29 11 0.26
30 14 0.33
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:5728403 original size:3 final size:3
Alignment explanation
Indices: 5728395--5728440 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5728385 GGCTTAAACT
5728395 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5728441 AAGCTAAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5741146 original size:21 final size:21
Alignment explanation
Indices: 5741122--5741184 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
5741112 CCGGTGAGCC
*
5741122 TTTTG-TTTCATG-GAAGCCAGT
1 TTTTGATTT-ATGCGAA-CCAGA
5741143 TTTTGATTTATGCGAACCAGA
1 TTTTGATTTATGCGAACCAGA
*
5741164 TTTTGATTTATGTGAACCAGA
1 TTTTGATTTATGCGAACCAGA
5741185 AACCTTAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 32 0.84
22 6 0.16
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (21 bp):
TTTTGATTTATGCGAACCAGA
Found at i:5745294 original size:30 final size:30
Alignment explanation
Indices: 5745255--5745317 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
5745245 ACACAACTAC
*
5745255 ACAAAAAAGCTTCATTTATGACCGCACAAG
1 ACAAAAAAGCTTCATTTATGACAGCACAAG
*
5745285 ACAAGAAAGCTTCATTTATGACAGCACAAG
1 ACAAAAAAGCTTCATTTATGACAGCACAAG
5745315 ACA
1 ACA
5745318 CGTTGTGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (30 bp):
ACAAAAAAGCTTCATTTATGACAGCACAAG
Found at i:5746480 original size:16 final size:16
Alignment explanation
Indices: 5746459--5746489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5746449 ACAGAGAGAA
5746459 AGAGAAAGAAAGGGAG
1 AGAGAAAGAAAGGGAG
*
5746475 AGAGAAAGAGAGGGA
1 AGAGAAAGAAAGGGA
5746490 CTCCCTCTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAGGGAG
Found at i:5747552 original size:23 final size:23
Alignment explanation
Indices: 5747518--5747573 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5747508 AAAAATTATG
* *
5747518 TTAATTTTTTATTTTGATTTAAT
1 TTAATTTATTATTTTGAATTAAT
*
5747541 TTAATTTATTATTTTTAATTAAT
1 TTAATTTATTATTTTGAATTAAT
**
5747564 AAAATTTATT
1 TTAATTTATT
5747574 TTGTTTAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTAATTTATTATTTTGAATTAAT
Found at i:5750063 original size:25 final size:25
Alignment explanation
Indices: 5750034--5750094 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
5750024 AAAAAATATT
*
5750034 TTAATTAATAATAA-TTAATTAATTA
1 TTAATT-ATAAAAATTTAATTAATTA
*
5750059 TTAATTATAAAAATTTACTTAA-T-
1 TTAATTATAAAAATTTAATTAATTA
5750082 TTAA-TATAAAAAT
1 TTAATTATAAAAAT
5750095 AAAAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 9 0.27
23 4 0.12
24 7 0.21
25 13 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTATAAAAATTTAATTAATTA
Found at i:5756490 original size:247 final size:245
Alignment explanation
Indices: 5756043--5756529 Score: 746
Period size: 247 Copynumber: 2.0 Consensus size: 245
5756033 TTCCAGTTTC
5756043 CTTTACAGGCTGCATCAACAGCATACAAGTGATAAGCTTAAAACATTATTGTTCTAAGTTCCACG
1 CTTTACAGGCTGCATCAACAGCATACAAGTGATAAGCTTAAAACATTATTGTTCTAAGTTCCACG
* * * *
5756108 ATACATAGCAAGCAAAGTTCTCAAAATCAATTTTCTGTTCCTTGATTTTAATTCCTGAATGCAAG
66 ATACATAGCAAGCAAAATTCTCAAAATCAATTTTCTGTTCCTAGATTTCAATTCCTCAATGCAAG
* * * **
5756173 TTCTGGCTAGATATAACAGATCTATGTCGTACTCATGAAAGTGCATAAAGCATGCCTCATCAAGT
131 TTCTGGCTAGATATAACAGATCTATGTCGCACACAGGAAAGTGCATAAAGCACACCTCATCAAGT
*
5756238 AAGAAATGACAAATCATGAGAACACACAAACCTACAGGGGGGAATAATTTT
196 AAGAAATGACAAATCAAGAGAACACACAAACCTACA-GGGGGAATAATTTT
* *
5756289 CTTTAACAGGCTGCATCAACAGCATACAAGTGATAAGTTTAAAGCATTATTGTTCTAAGTTCCA-
1 CTTT-ACAGGCTGCATCAACAGCATACAAGTGATAAGCTTAAAACATTATTGTTCTAAGTTCCAC
* *
5756353 GAATGA-ATAGCAAGCAAAATTCTCACAATCAATTTTCTG-TCTCTAGATTTCAATTCCTCAATT
65 G-AT-ACATAGCAAGCAAAATTCTCAAAATCAATTTTCTGTTC-CTAGATTTCAATTCCTCAATG
*
5756416 CAAGTTCTGGCTAGATATAACAGATCTATGTGGCACACAGGAAAGTGCATAAAGCACACCTCATC
127 CAAGTTCTGGCTAGATATAACAGATCTATGTCGCACACAGGAAAGTGCATAAAGCACACCTCATC
* **
5756481 AATTAAGAAATGACAAATCAAGAGAGTACACAAACCTACAGGGGGAATA
192 AAGTAAGAAATGACAAATCAAGAGAACACACAAACCTACAGGGGGAATA
5756530 CTTTAAATAG
Statistics
Matches: 219, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
246 16 0.07
247 202 0.92
248 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (245 bp):
CTTTACAGGCTGCATCAACAGCATACAAGTGATAAGCTTAAAACATTATTGTTCTAAGTTCCACG
ATACATAGCAAGCAAAATTCTCAAAATCAATTTTCTGTTCCTAGATTTCAATTCCTCAATGCAAG
TTCTGGCTAGATATAACAGATCTATGTCGCACACAGGAAAGTGCATAAAGCACACCTCATCAAGT
AAGAAATGACAAATCAAGAGAACACACAAACCTACAGGGGGAATAATTTT
Found at i:5760554 original size:19 final size:19
Alignment explanation
Indices: 5760504--5760555 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
5760494 CTTTTTTAGC
* *
5760504 TTTAATTAT-ATATAAATT
1 TTTAATTATAAAATAAATA
*
5760522 TATTAATTTTTAAAATAAATA
1 T-TTAA-TTATAAAATAAATA
5760543 TTTAATTATAAAA
1 TTTAATTATAAAA
5760556 AAACATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.04
19 11 0.41
20 7 0.26
21 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATTATAAAATAAATA
Found at i:5774158 original size:27 final size:28
Alignment explanation
Indices: 5774128--5774184 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
5774118 TTTTAAATTA
5774128 TTTTAAAAAATTCAAATAAAT-GTTATT
1 TTTTAAAAAATTCAAATAAATCGTTATT
* * * *
5774155 TTTTATAACATTCAATTAAATCTTTATT
1 TTTTAAAAAATTCAAATAAATCGTTATT
5774183 TT
1 TT
5774185 AGACTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTTAAAAAATTCAAATAAATCGTTATT
Found at i:5778196 original size:24 final size:23
Alignment explanation
Indices: 5778153--5778198 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5778143 AGCTAGAGAG
*
5778153 AAAAAACAAAAGGAAAAAGAAAT
1 AAAAAAAAAAAGGAAAAAGAAAT
*
5778176 AAAAAAAAAAAGAGAACAAGAAA
1 AAAAAAAAAAAG-GAAAAAGAAA
5778199 AATCAAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAGGAAAAAGAAAT
Found at i:5785713 original size:26 final size:26
Alignment explanation
Indices: 5785681--5785755 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 26
5785671 TATATTTTAT
5785681 TTTTATTTTTATTATAATTTTATATA
1 TTTTATTTTTATTATAATTTTATATA
* * *
5785707 TTTTATTTTCTTAATAAAATTTTTTATA
1 TTTTA-TTT-TTATTATAATTTTATATA
* *
5785735 TTATATATTTTATTTTAATTT
1 TTTTAT-TTTTATTATAATTT
5785756 CTTTTTCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 5 0.13
27 13 0.33
28 21 0.54
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTATTTTTATTATAATTTTATATA
Found at i:5786849 original size:2 final size:2
Alignment explanation
Indices: 5786842--5786867 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5786832 GACTGTATTT
5786842 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5786868 ATACTTCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5795026 original size:26 final size:26
Alignment explanation
Indices: 5794990--5795053 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
5794980 ACGTAACATT
5794990 ACAATGATATGAAATATTCATATAAA
1 ACAATGATATGAAATATTCATATAAA
*
5795016 ACAATGATATGACATATTCATATAAA
1 ACAATGATATGAAATATTCATATAAA
* *
5795042 ATAATAATATGA
1 ACAATGATATGA
5795054 TCTCATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (26 bp):
ACAATGATATGAAATATTCATATAAA
Found at i:5803598 original size:5 final size:5
Alignment explanation
Indices: 5803590--5803618 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5803580 ACTTATCGTA
5803590 TCTGG TCTGG TCTGG TCTGG TCTGG TCTG
1 TCTGG TCTGG TCTGG TCTGG TCTGG TCTG
5803619 CGGTAGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.38, T:0.41
Consensus pattern (5 bp):
TCTGG
Found at i:5813089 original size:2 final size:2
Alignment explanation
Indices: 5813084--5813111 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5813074 ATAAAGAGTA
5813084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5813112 TTTCTGTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5815729 original size:14 final size:15
Alignment explanation
Indices: 5815692--5815729 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
5815682 TTTTTAGGAA
5815692 AAAAAAAAGAAAAGGG
1 AAAAAAAAG-AAAGGG
*
5815708 AAAGAAAAG-AAGGG
1 AAAAAAAAGAAAGGG
5815722 AAAAAAAA
1 AAAAAAAA
5815730 TATTGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
16 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAGGG
Found at i:5820304 original size:17 final size:17
Alignment explanation
Indices: 5820284--5820318 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5820274 TTTAGTTTTT
5820284 TATTAT-TTTTTAAATAA
1 TATTATATTTTT-AATAA
5820301 TATTATATTTTTAATAA
1 TATTATATTTTTAATAA
5820318 T
1 T
5820319 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATTTTTAATAA
Found at i:5829442 original size:17 final size:19
Alignment explanation
Indices: 5829420--5829455 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
5829410 TTTGTGCTTC
5829420 CTTGAT-TGTAA-TTTTCT
1 CTTGATATGTAAGTTTTCT
5829437 CTTGATATGTAAGTTTTCT
1 CTTGATATGTAAGTTTTCT
5829456 ATGTCTACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (19 bp):
CTTGATATGTAAGTTTTCT
Found at i:5834523 original size:21 final size:18
Alignment explanation
Indices: 5834497--5834535 Score: 51
Period size: 21 Copynumber: 2.0 Consensus size: 18
5834487 GCCTATAGAA
5834497 GAGGAAGACAATGACTAAGGT
1 GAGGAAG-CAA-GAC-AAGGT
5834518 GAGGAAGCAAGACAAGGT
1 GAGGAAGCAAGACAAGGT
5834536 TCATTCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 3 0.17
21 7 0.39
ACGTcount: A:0.44, C:0.10, G:0.36, T:0.10
Consensus pattern (18 bp):
GAGGAAGCAAGACAAGGT
Found at i:5835962 original size:22 final size:22
Alignment explanation
Indices: 5835937--5835982 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5835927 GAGCACCATC
*
5835937 ATCTCCCACAAATCAGCAACAA
1 ATCTCCCACAAAACAGCAACAA
*
5835959 ATCTCCCATAAAACAGCAACAA
1 ATCTCCCACAAAACAGCAACAA
5835981 AT
1 AT
5835983 TACTCACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.33, G:0.04, T:0.15
Consensus pattern (22 bp):
ATCTCCCACAAAACAGCAACAA
Found at i:5836015 original size:22 final size:22
Alignment explanation
Indices: 5835990--5836032 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5835980 AATTACTCAC
*
5835990 CAAACCAGCAGCAGATCAGCAT
1 CAAACCAGCAGCAAATCAGCAT
5836012 CAAACCAGCAGCAAATCAGCA
1 CAAACCAGCAGCAAATCAGCA
5836033 ACAGACATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.33, G:0.16, T:0.07
Consensus pattern (22 bp):
CAAACCAGCAGCAAATCAGCAT
Found at i:5836046 original size:45 final size:44
Alignment explanation
Indices: 5835997--5836180 Score: 215
Period size: 45 Copynumber: 4.3 Consensus size: 44
5835987 CACCAAACCA
5835997 GCAGCAGATCAGCATCAAACCAGCAGCAAATCAGCAACAGACATG
1 GCAGCAGATCAGCA-CAAACCAGCAGCAAATCAGCAACAGACATG
*
5836042 GCAGCATATCAG--C--A-C--CA--AAATCAGCAACAGACATG
1 GCAGCAGATCAGCACAAACCAGCAGCAAATCAGCAACAGACATG
* * *
5836077 GCAGCAGATCAGCAACAAACCAACAACAAATTAGCAACAGACATG
1 GCAGCAGATCAGC-ACAAACCAGCAGCAAATCAGCAACAGACATG
* **
5836122 GCAGCATATCAGCACCAAACCAGCAGCAAATCAGTGACAGACATG
1 GCAGCAGATCAGCA-CAAACCAGCAGCAAATCAGCAACAGACATG
5836167 GCAGCAGATCAGCA
1 GCAGCAGATCAGCA
5836181 ACAACAATAA
Statistics
Matches: 118, Mismatches: 10, Indels: 22
0.79 0.07 0.15
Matches are distributed among these distances:
35 29 0.25
37 2 0.02
38 1 0.01
39 1 0.01
40 2 0.02
41 1 0.01
42 1 0.01
43 2 0.02
44 1 0.01
45 78 0.66
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.10
Consensus pattern (44 bp):
GCAGCAGATCAGCACAAACCAGCAGCAAATCAGCAACAGACATG
Found at i:5836064 original size:35 final size:35
Alignment explanation
Indices: 5836024--5836140 Score: 126
Period size: 35 Copynumber: 3.1 Consensus size: 35
5836014 AACCAGCAGC
5836024 AAATCAGCAACAGACATGGCAGCATATCAGCACCA
1 AAATCAGCAACAGACATGGCAGCATATCAGCACCA
*
5836059 AAATCAGCAACAGACATGGCAGCAGATCAGCAACAAACCAACAA
1 AAATCAGCAACAGACATGGCAGCATATCAG---C--A-C--C-A
*
5836103 CAAATTAGCAACAGACATGGCAGCATATCAGCACCA
1 -AAATCAGCAACAGACATGGCAGCATATCAGCACCA
5836139 AA
1 AA
5836141 CCAGCAGCAA
Statistics
Matches: 69, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
35 31 0.45
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 2 0.03
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
45 28 0.41
ACGTcount: A:0.46, C:0.27, G:0.16, T:0.10
Consensus pattern (35 bp):
AAATCAGCAACAGACATGGCAGCATATCAGCACCA
Found at i:5836091 original size:23 final size:23
Alignment explanation
Indices: 5836059--5836183 Score: 105
Period size: 23 Copynumber: 5.5 Consensus size: 23
5836049 ATCAGCACCA
5836059 AAATCAGCAACAGACATGGCAGC
1 AAATCAGCAACAGACATGGCAGC
* * * *
5836082 AGATCAGCAACAAACCA--ACAAC
1 AAATCAGCAACAGA-CATGGCAGC
*
5836104 AAATTAGCAACAGACATGGCAGC
1 AAATCAGCAACAGACATGGCAGC
* * *
5836127 ATATCAGCACCAAACCA--GCAGC
1 AAATCAGCAACAGA-CATGGCAGC
**
5836149 AAATCAGTGACAGACATGGCAGC
1 AAATCAGCAACAGACATGGCAGC
*
5836172 AGATCAGCAACA
1 AAATCAGCAACA
5836184 ACAATAACAG
Statistics
Matches: 75, Mismatches: 21, Indels: 12
0.69 0.19 0.11
Matches are distributed among these distances:
21 4 0.05
22 28 0.37
23 39 0.52
24 4 0.05
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.10
Consensus pattern (23 bp):
AAATCAGCAACAGACATGGCAGC
Found at i:5859734 original size:20 final size:20
Alignment explanation
Indices: 5859690--5859735 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5859680 TGAACATTTA
5859690 ATTTA-AAAAATATTTTATT
1 ATTTATAAAAATATTTTATT
*
5859709 AATTATAAAAATATTTTAATT
1 ATTTATAAAAATATTTT-ATT
5859730 -TTTATA
1 ATTTATA
5859736 TATTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTATAAAAATATTTTATT
Found at i:5873354 original size:15 final size:16
Alignment explanation
Indices: 5873334--5873378 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
5873324 TAAAGTTTTG
5873334 TTATATTTT-TTTAAT
1 TTATATTTTATTTAAT
5873349 TTATATTATTATTT-AT
1 TTATATT-TTATTTAAT
*
5873365 TTTTATTTTATTTA
1 TTATATTTTATTTA
5873379 CTCATATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 13 0.50
16 10 0.38
17 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATATTTTATTTAAT
Found at i:5873361 original size:21 final size:21
Alignment explanation
Indices: 5873329--5873376 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5873319 AATTCTAAAG
*
5873329 TTTTGTTA-TATTT-TTTTAA
1 TTTTATTATTATTTATTTTAA
*
5873348 TTTATATTATTATTTATTTTTA
1 TTT-TATTATTATTTATTTTAA
5873370 TTTTATT
1 TTTTATT
5873377 TACTCATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 4 0.17
21 9 0.38
22 8 0.33
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTATTATTATTTATTTTAA
Found at i:5882422 original size:30 final size:30
Alignment explanation
Indices: 5882349--5882426 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
5882339 AGCAATGGGA
**
5882349 CCTGGTGGACCGGGAGGAGGGCCAGGAGGT
1 CCTGGTGGATGGGGAGGAGGGCCAGGAGGT
5882379 CCTGGTGGATGGGGAGGAGGGCCAGGAGGT
1 CCTGGTGGATGGGGAGGAGGGCCAGGAGGT
*
5882409 CCTGGTGGTTGGGGAGGA
1 CCTGGTGGATGGGGAGGA
5882427 CCAGGGGGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.15, C:0.15, G:0.55, T:0.14
Consensus pattern (30 bp):
CCTGGTGGATGGGGAGGAGGGCCAGGAGGT
Found at i:5882439 original size:27 final size:27
Alignment explanation
Indices: 5882364--5882449 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 27
5882354 TGGACCGGGA
* *
5882364 GGAGGGCCAGGAGGTCCTGGTGGATGG
1 GGAGGACCAGGAGGTCCTGGTGGTTGG
5882391 GGAGGAGGGCCAGGAGGTCCTGGTGGTTGG
1 GGAGGA---CCAGGAGGTCCTGGTGGTTGG
* * *
5882421 GGAGGACCAGGGGGGCCTGGCGGTTGG
1 GGAGGACCAGGAGGTCCTGGTGGTTGG
5882448 GG
1 GG
5882450 TCCTGGTCCG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 25 0.49
30 26 0.51
ACGTcount: A:0.13, C:0.15, G:0.58, T:0.14
Consensus pattern (27 bp):
GGAGGACCAGGAGGTCCTGGTGGTTGG
Found at i:5882482 original size:30 final size:29
Alignment explanation
Indices: 5882430--5882491 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
5882420 GGGAGGACCA
* *
5882430 GGGGGGCCTGGCGGTTGGGGTCCTGGTCC
1 GGGGGGCCTGGCGGTTGGGGTCCAGGGCC
*
5882459 GGGGGGACCTGGCGGATT-TGGTCCAGGGCC
1 GGGGGG-CCTGGCGG-TTGGGGTCCAGGGCC
5882489 GGG
1 GGG
5882492 AGGTCCCTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 20 0.71
31 2 0.07
ACGTcount: A:0.05, C:0.23, G:0.55, T:0.18
Consensus pattern (29 bp):
GGGGGGCCTGGCGGTTGGGGTCCAGGGCC
Found at i:5886293 original size:2 final size:2
Alignment explanation
Indices: 5886286--5886310 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5886276 TTCATATCAG
5886286 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5886311 TACTTACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5886421 original size:2 final size:2
Alignment explanation
Indices: 5886414--5886442 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5886404 TACTCTAATC
5886414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5886443 GTTTGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5891929 original size:27 final size:29
Alignment explanation
Indices: 5891898--5891952 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
5891888 TTTTAAACTG
5891898 TAACAA-AA-TGTTTTTGAATATGACATA
1 TAACAATAATTGTTTTTGAATATGACATA
* *
5891925 TAACAATAATTTTTTTTTAATATGACAT
1 TAACAATAATTGTTTTTGAATATGACAT
5891953 GTAAAAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 2 0.08
29 16 0.67
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (29 bp):
TAACAATAATTGTTTTTGAATATGACATA
Found at i:5892015 original size:21 final size:21
Alignment explanation
Indices: 5891990--5892086 Score: 106
Period size: 21 Copynumber: 4.5 Consensus size: 21
5891980 TATTTTTATA
5891990 CATGACGTGTAACAACCTAAT
1 CATGACGTGTAACAACCTAAT
* * *
5892011 TATGACATGTAACATATTCTTATAT
1 CATGACGTGTAACA-A--CCTA-AT
*
5892036 -ATGACGTGTAACAACTTAAT
1 CATGACGTGTAACAACCTAAT
*
5892056 CATGACGTGTAACAACTTAAT
1 CATGACGTGTAACAACCTAAT
5892077 CATGACGTGT
1 CATGACGTGT
5892087 CACATGTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
20 2 0.03
21 46 0.69
22 1 0.01
23 1 0.01
24 15 0.22
25 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (21 bp):
CATGACGTGTAACAACCTAAT
Found at i:5892026 original size:45 final size:45
Alignment explanation
Indices: 5891977--5892069 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
5891967 ATAACGTATT
* *
5891977 ACATATTTTTATACATGACGTGTAACAACCTAATTATGACATGTA
1 ACATATTCTTATACATGACGTGTAACAACCTAATCATGACATGTA
* * *
5892022 ACATATTCTTATATATGACGTGTAACAACTTAATCATGACGTGTA
1 ACATATTCTTATACATGACGTGTAACAACCTAATCATGACATGTA
5892067 ACA
1 ACA
5892070 ACTTAATCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
ACATATTCTTATACATGACGTGTAACAACCTAATCATGACATGTA
Found at i:5892135 original size:24 final size:24
Alignment explanation
Indices: 5892077--5892138 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
5892067 ACAACTTAAT
* *
5892077 CATGACGTGTCACATGTTTTTGTA
1 CATGACGTATAACATGTTTTTGTA
* *
5892101 TAT-ATCATATAACATGTTTTTGTA
1 CATGA-CGTATAACATGTTTTTGTA
5892125 CATGACGTATAACA
1 CATGACGTATAACA
5892139 ACCTAATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (24 bp):
CATGACGTATAACATGTTTTTGTA
Found at i:5897475 original size:2 final size:2
Alignment explanation
Indices: 5897468--5897512 Score: 56
Period size: 2 Copynumber: 22.0 Consensus size: 2
5897458 TGCACCCATG
*
5897468 TA TA TA TA TA TA TA TA TA TT TA TA GTA GTA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA TA TA TA
5897511 TA
1 TA
5897513 ATTTGCCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 33 0.85
3 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5897960 original size:30 final size:30
Alignment explanation
Indices: 5897926--5897987 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
5897916 CAAAATTAAA
*
5897926 TTTGTTATTAAGAAAGAACACAAAAAA-TGT
1 TTTGTTATTAAAAAAGAACA-AAAAAATTGT
* *
5897956 TTTGTTGTTAAAAAATAACAAAAAAATTGT
1 TTTGTTATTAAAAAAGAACAAAAAAATTGT
5897986 TT
1 TT
5897988 GGTGGACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.35
Consensus pattern (30 bp):
TTTGTTATTAAAAAAGAACAAAAAAATTGT
Found at i:5898819 original size:2 final size:2
Alignment explanation
Indices: 5898812--5898839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5898802 TCTTTTCCTT
5898812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5898840 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5905784 original size:33 final size:33
Alignment explanation
Indices: 5905727--5905801 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
5905717 TTTATAATGT
5905727 TATAAT-TAAAATAAAAAAATTAAAACAAAATA
1 TATAATATAAAATAAAAAAATTAAAACAAAATA
* *
5905759 TATAATATAAGAATCAAAAAA-TAAAATAAAATA
1 TATAATATAA-AATAAAAAAATTAAAACAAAATA
5905792 -A-AATATAAAA
1 TATAATATAAAA
5905802 AATTAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 2 0.05
31 7 0.18
32 7 0.18
33 14 0.36
34 9 0.23
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (33 bp):
TATAATATAAAATAAAAAAATTAAAACAAAATA
Found at i:5905818 original size:26 final size:24
Alignment explanation
Indices: 5905753--5905852 Score: 69
Period size: 24 Copynumber: 4.1 Consensus size: 24
5905743 AAATTAAAAC
* *
5905753 AAAATATA-TAATATAAGAAT-CAA
1 AAAATAAATTAATATAA-AATATAA
* *
5905776 AAAATAAAATAAAATAAAATATAA
1 AAAATAAATTAATATAAAATATAA
* * ***
5905800 AAAATTAAAATTTATATAATATAGGT
1 AAAA-T-AAATTAATATAAAATATAA
*
5905826 AAAATAAATTAATATATAATATAA
1 AAAATAAATTAATATAAAATATAA
5905850 AAA
1 AAA
5905853 TTAGATCAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
23 10 0.18
24 29 0.51
25 2 0.04
26 16 0.28
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (24 bp):
AAAATAAATTAATATAAAATATAA
Found at i:5906156 original size:15 final size:15
Alignment explanation
Indices: 5906133--5906187 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
5906123 ATTTTCCCTG
* *
5906133 CAATAACATTACTTA
1 CAATCACATTACCTA
*
5906148 CAATCACATTACCTG
1 CAATCACATTACCTA
* *
5906163 CAATCACATTATCTG
1 CAATCACATTACCTA
*
5906178 TAATCACATT
1 CAATCACATT
5906188 GTATTGTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (15 bp):
CAATCACATTACCTA
Found at i:5907152 original size:45 final size:47
Alignment explanation
Indices: 5907056--5907173 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 47
5907046 TAATATGGCA
* * * * *
5907056 TATAACAACCTAATCATGATATATCACATGTTTTTGTACATGACGTG
1 TATAACAACCTAACCATGATATGTAACATATTTTTATACATGACGTG
*
5907103 --TAACAACCTAACCATGATATGTAACATATTTTTATATAT-A-GTG
1 TATAACAACCTAACCATGATATGTAACATATTTTTATACATGACGTG
* **
5907146 TATAACAAACTAACCATGACGTGTAACA
1 TATAACAACCTAACCATGATATGTAACA
5907174 ACCTAATTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
43 3 0.05
44 1 0.02
45 56 0.93
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (47 bp):
TATAACAACCTAACCATGATATGTAACATATTTTTATACATGACGTG
Found at i:5907173 original size:21 final size:21
Alignment explanation
Indices: 5907148--5907194 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5907138 ATATAGTGTA
*
5907148 TAACAAACTAACCATGACGTG
1 TAACAAACTAACCATAACGTG
* **
5907169 TAACAACCTAATTATAACGTG
1 TAACAAACTAACCATAACGTG
5907190 TAACA
1 TAACA
5907195 TGTTTTTGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (21 bp):
TAACAAACTAACCATAACGTG
Found at i:5907192 original size:66 final size:66
Alignment explanation
Indices: 5907094--5907230 Score: 166
Period size: 66 Copynumber: 2.1 Consensus size: 66
5907084 TGTTTTTGTA
* * **
5907094 CATGACGTGTAACAACCTAACCATGATATGTAACATATTTTTATATATAGTGTATAACAAACTAA
1 CATGACGTGTAACAACCTAACCATAACATGTAACATATTTTTATATATAGCATATAACAAACTAA
5907159 C
66 C
** * * * * *
5907160 CATGACGTGTAACAACCTAATTATAACGTGTAACATGTTTTTGTATATCGCATATAACAACCTAA
1 CATGACGTGTAACAACCTAACCATAACATGTAACATATTTTTATATATAGCATATAACAAACTAA
5907225 C
66 C
*
5907226 AATGA
1 CATGA
5907231 TATGTCACAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (66 bp):
CATGACGTGTAACAACCTAACCATAACATGTAACATATTTTTATATATAGCATATAACAAACTAA
C
Found at i:5907218 original size:45 final size:45
Alignment explanation
Indices: 5907169--5907408 Score: 203
Period size: 45 Copynumber: 5.3 Consensus size: 45
5907159 CCATGACGTG
** * * * *
5907169 TAACAACCTAATTATAACGTGTAACATGTTTTTGTATATCGCATA
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTACATAGCATA
* ** * ** *
5907214 TAACAACCTAACAATGATATGTCACATGGTTTTGTACAGGGCATG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTACATAGCATA
* * * * *
5907259 TAAAAACCTAACCATGACTTGTCATATGTTTTTGTACATGGCGTA
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTACATAGCATA
* * * * *
5907304 TAACAATCTAACCATGGCGTGTCACATGTTTATGTACATAGTATG
1 TAACAACCTAACCATGACGTGTCACATGTTTTTGTACATAGCATA
* * * * * *
5907349 TAACAATCTAATCAT-AGCGTGTCATATGGTTTTGTATATAGCGTA
1 TAACAACCTAACCATGA-CGTGTCACATGTTTTTGTACATAGCATA
5907394 TAACAACCTAACCAT
1 TAACAACCTAACCAT
5907409 AACTTGATAA
Statistics
Matches: 153, Mismatches: 41, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
45 153 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (45 bp):
TAACAACCTAACCATGACGTGTCACATGTTTTTGTACATAGCATA
Found at i:5907406 original size:90 final size:90
Alignment explanation
Indices: 5907167--5907408 Score: 263
Period size: 90 Copynumber: 2.7 Consensus size: 90
5907157 AACCATGACG
* * * * * * * *
5907167 TGTAACAACCTAATTATAACGTGTAACATGTTTTTGTATATCGCATATAACAACCTAACAATGAT
1 TGTAACAACCTAATCATAGCGTGTCATATGTTTTTGTATATAGCGTATAACAACCTAACCATGAC
*
5907232 ATGTCACATGGTTTTGTACAGGGCA
66 ATGTCACATGGTTTTGTACAGAGCA
* * * * * * *
5907257 TGTAAAAACCTAACCAT-GACTTGTCATATGTTTTTGTACATGGCGTATAACAATCTAACCATGG
1 TGTAACAACCTAATCATAG-CGTGTCATATGTTTTTGTATATAGCGTATAACAACCTAACCATGA
* * *
5907321 CGTGTCACAT-GTTTATGTACATAGTA
65 CATGTCACATGGTTT-TGTACAGAGCA
* *
5907347 TGTAACAATCTAATCATAGCGTGTCATATGGTTTTGTATATAGCGTATAACAACCTAACCAT
1 TGTAACAACCTAATCATAGCGTGTCATATGTTTTTGTATATAGCGTATAACAACCTAACCAT
5907409 AACTTGATAA
Statistics
Matches: 123, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
89 4 0.03
90 118 0.96
91 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (90 bp):
TGTAACAACCTAATCATAGCGTGTCATATGTTTTTGTATATAGCGTATAACAACCTAACCATGAC
ATGTCACATGGTTTTGTACAGAGCA
Found at i:5907603 original size:23 final size:23
Alignment explanation
Indices: 5907559--5907604 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5907549 TTATGCTCTC
**
5907559 GATTTCTCTCTCTCGCTTTTTCA
1 GATTTCTCTCTCTCGCACTTTCA
* *
5907582 GATTTCTCTTTCTTGCACTTTCA
1 GATTTCTCTCTCTCGCACTTTCA
5907605 AGACACCAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.28, G:0.09, T:0.52
Consensus pattern (23 bp):
GATTTCTCTCTCTCGCACTTTCA
Found at i:5908053 original size:45 final size:45
Alignment explanation
Indices: 5908016--5908101 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
5908006 ATTTTTTAAT
* * *
5908016 ATGATATGTAACAACCTAATCATGATATATCACATATTTTTGTAC
1 ATGACATGTAACAACCTAACCATGATATATAACATATTTTTGTAC
* *
5908061 ATGACGTGTAACAACCTAACCATGATATGTAACATATTTTT
1 ATGACATGTAACAACCTAACCATGATATATAACATATTTTT
5908102 ATATATACCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (45 bp):
ATGACATGTAACAACCTAACCATGATATATAACATATTTTTGTAC
Found at i:5908118 original size:45 final size:45
Alignment explanation
Indices: 5908024--5908139 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 45
5908014 ATATGATATG
* * * * *
5908024 TAACAACCTAATCATGATATATCACATATTTTTGTACATGACGTG
1 TAACAACCTAACCATGATATGTAACATATTTTTATACATGACGTA
*
5908069 TAACAACCTAACCATGATATGTAACATATTTTTATATAT-ACCGTA
1 TAACAACCTAACCATGATATGTAACATATTTTTATACATGA-CGTA
* * **
5908114 TAACAAACTAACAATGACGTGTAACA
1 TAACAACCTAACCATGATATGTAACA
5908140 ACCTAATTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.02
45 59 0.98
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (45 bp):
TAACAACCTAACCATGATATGTAACATATTTTTATACATGACGTA
Found at i:5908131 original size:66 final size:66
Alignment explanation
Indices: 5908061--5908196 Score: 173
Period size: 66 Copynumber: 2.1 Consensus size: 66
5908051 ATTTTTGTAC
* * *
5908061 ATGACGTGTAACAACCTAACCATGATATGTAACATATTTTTATATATACCGTATAACAAACTAAC
1 ATGACGTGTAACAACCTAACCATAACATGTAACATATTTTTATACATACCGTATAACAAACTAAC
5908126 A
66 A
** * * * ** *
5908127 ATGACGTGTAACAACCTAATTATAACGTGTAACATGTTTTTGTACATTGCGTATAACAACCTAAC
1 ATGACGTGTAACAACCTAACCATAACATGTAACATATTTTTATACATACCGTATAACAAACTAAC
5908192 A
66 A
5908193 ATGA
1 ATGA
5908197 TATGTGACAT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (66 bp):
ATGACGTGTAACAACCTAACCATAACATGTAACATATTTTTATACATACCGTATAACAAACTAAC
A
Found at i:5908139 original size:21 final size:21
Alignment explanation
Indices: 5908114--5908160 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5908104 ATATACCGTA
*
5908114 TAACAAACTAACAATGACGTG
1 TAACAAACTAACAATAACGTG
* **
5908135 TAACAACCTAATTATAACGTG
1 TAACAAACTAACAATAACGTG
5908156 TAACA
1 TAACA
5908161 TGTTTTTGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (21 bp):
TAACAAACTAACAATAACGTG
Found at i:5908289 original size:24 final size:24
Alignment explanation
Indices: 5908250--5908299 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
5908240 GACTTATCAT
* *
5908250 ATGTTTTTGTAGATGGAGTATAAC
1 ATGTTTTTATACATGGAGTATAAC
* *
5908274 ATGTTTTTATACATGGTGTGTAAC
1 ATGTTTTTATACATGGAGTATAAC
5908298 AT
1 AT
5908300 CATGACGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (24 bp):
ATGTTTTTATACATGGAGTATAAC
Found at i:5909110 original size:31 final size:30
Alignment explanation
Indices: 5909072--5909146 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
5909062 AACCCAAAAA
*
5909072 AAAATAAAAAATAATTTTTTTATAATTAATT
1 AAAATAAAAAATAATATTTTTAT-ATTAATT
*
5909103 AAAATAAAATAT-ATATTTTTATATTAATT
1 AAAATAAAAAATAATATTTTTATATTAATT
* *
5909132 ATTAATTAAAAATAA
1 A-AAATAAAAAATAA
5909147 AAACATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 8 0.22
30 17 0.46
31 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATAAAAAATAATATTTTTATATTAATT
Found at i:5909136 original size:32 final size:31
Alignment explanation
Indices: 5909072--5909136 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
5909062 AACCCAAAAA
*
5909072 AAAATAAAAAATAATTTTTTTATAATTAATT
1 AAAATAAAAAATAATTTTTATATAATTAATT
*
5909103 AAAATAAAATATATATTTTTATATTAATT-ATT
1 AAAATAAAAAATA-ATTTTTATA-TAATTAATT
5909135 AA
1 AA
5909137 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 12 0.40
32 13 0.43
33 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
AAAATAAAAAATAATTTTTATATAATTAATT
Found at i:5909144 original size:32 final size:30
Alignment explanation
Indices: 5909072--5909146 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 30
5909062 AACCCAAAAA
*
5909072 AAAATAAAAAATAATTTTTTTATAATTAATT
1 AAAAT-AAAAATAATATTTTTATAATTAATT
5909103 AAAAT-AAAATATATATTTTTAT-ATTAATT
1 AAAATAAAAATA-ATATTTTTATAATTAATT
*
5909132 ATTAATTAAAAATAA
1 A--AAATAAAAATAA
5909147 AAACATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 14 0.37
30 9 0.24
31 9 0.24
32 6 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATAAAAATAATATTTTTATAATTAATT
Found at i:5909173 original size:190 final size:191
Alignment explanation
Indices: 5908724--5909189 Score: 644
Period size: 189 Copynumber: 2.5 Consensus size: 191
5908714 TATAATTTTT
* * *
5908724 AAATAAAATAGATATTTTTATATTAATTTATTTATTAAAAAATAAAAACATTTATAATGTTAAAA
1 AAATAAAATATATATTTTTATATTAATTTATTAATTAAAAAATAAAAACATTTATCATGTTAAAA
* **
5908789 TTAAAAGGGAATTCAATTTTTTTAGCATTTTTTTGTTGAAAATCTAAAGATTGAAACTCATAAAA
66 TTAAAAGGGAATTTAATTTTTTTAGCATTTTTTCCTTGAAAATCTAAAGATTGAAACTCATAAAA
* * *
5908854 AATCATTTTTCACTTTTCAACTAAAAAATTAATTAAAAAAATAATTTGTTGATAATTAATTA
131 AATAATTTTTCACTTTTCAACCAAAAAA-TAAATAAAAAAATAATTTGTTGATAATTAATTA
* * *
5908916 GAAT-AAA-ATATATTTTT-TATTAATTTATTAATTAAAAAATAAAAACA-TTGTCATATTAAAA
1 AAATAAAATATATATTTTTATATTAATTTATTAATTAAAAAATAAAAACATTTATCATGTTAAAA
** * * *
5908977 TTAAAAGGGAATTTTCTGTTTTTTAGTATTTTTTCCTTTACAATCTAAAGATTGAAACTCATAAA
66 TTAAAAGGGAATTTAAT-TTTTTTAGCATTTTTTCCTTGAAAATCTAAAGATTGAAACTCAT-AA
* *
5909042 AAAATAATTTTTCA-TGTTTCAACCCAAAAAA-AAAT-AAAAAATAATTTTTTTATAATTAATTA
129 AAAATAATTTTTCACT-TTTCAA-CCAAAAAATAAATAAAAAAATAATTTGTTGATAATTAATTA
5909104 AAATAAAATATATATTTTTATATTAA-TTATTAATT-AAAAATAAAAACATTTATCATGTTAAAA
1 AAATAAAATATATATTTTTATATTAATTTATTAATTAAAAAATAAAAACATTTATCATGTTAAAA
*
5909167 TTAAAAGGGAATTTGATTTTTTT
66 TTAAAAGGGAATTTAATTTTTTT
5909190 TGTTTAAAAT
Statistics
Matches: 242, Mismatches: 24, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
188 53 0.22
189 94 0.39
190 76 0.31
191 16 0.07
192 3 0.01
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (191 bp):
AAATAAAATATATATTTTTATATTAATTTATTAATTAAAAAATAAAAACATTTATCATGTTAAAA
TTAAAAGGGAATTTAATTTTTTTAGCATTTTTTCCTTGAAAATCTAAAGATTGAAACTCATAAAA
AATAATTTTTCACTTTTCAACCAAAAAATAAATAAAAAAATAATTTGTTGATAATTAATTA
Found at i:5913592 original size:35 final size:35
Alignment explanation
Indices: 5913553--5913619 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
5913543 ACAAGTACAC
* *
5913553 CCTGTGGAAGTCAAAAAAACATTTCAGGAAACAAA
1 CCTGTGAAAGTCAAAAAAACATTTAAGGAAACAAA
5913588 CCTGTGAAAGTCAAAAAAACATTTAAGGAAAC
1 CCTGTGAAAGTCAAAAAAACATTTAAGGAAAC
5913620 GAACTACTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (35 bp):
CCTGTGAAAGTCAAAAAAACATTTAAGGAAACAAA
Found at i:5916640 original size:25 final size:25
Alignment explanation
Indices: 5916612--5916659 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5916602 AAATATTTTT
* *
5916612 TTATTAATAAACGTAATTATAGGAA
1 TTATAAATAAACATAATTATAGGAA
* *
5916637 TTATAAATTATCATAATTATAGG
1 TTATAAATAAACATAATTATAGG
5916660 GATTGGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (25 bp):
TTATAAATAAACATAATTATAGGAA
Found at i:5916676 original size:25 final size:25
Alignment explanation
Indices: 5916625--5916713 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
5916615 TTAATAAACG
* ** * *
5916625 TAATTATAGGAATTATAAATTATCA
1 TAATTATAGGGATTAGGAATCACCA
* *
5916650 TAATTATAGGGATTGGGAGTCACCA
1 TAATTATAGGGATTAGGAATCACCA
** *
5916675 TAATTATAGAAATTAGGAATCATCA
1 TAATTATAGGGATTAGGAATCACCA
*
5916700 TAATTGTAGGGATT
1 TAATTATAGGGATT
5916714 TTTATTTTCT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (25 bp):
TAATTATAGGGATTAGGAATCACCA
Found at i:5917024 original size:198 final size:199
Alignment explanation
Indices: 5916678--5917073 Score: 654
Period size: 198 Copynumber: 2.0 Consensus size: 199
5916668 GTCACCATAA
5916678 TTATAGAAATTAGGAATCATCATAATTGTAGGGATTTTTATTTTCTTTATTTTCTTTATTCTTTT
1 TTATAGAAATTAGGAATCATCATAATTGTAGGGATTTTTATTTTCTTTATTTTCTTTATTCTTTT
* * *
5916743 TCTATTTTAGAGATGTGTAGGCTATATATATAGGTGATTTATTATGAATGAAAGGTGTGGAGTTT
66 TCTATTTTAGAAATGTGTAGGCTATATATATAGGTGATTTATTATGAATAAAAGGTGTGAAGTTT
* * * *
5916808 TCTCTTCCTAACTAACATGGTATCAGAGCAGTTTTGGCAGATCTGTTTCCTTTGAAACAGAGTTC
131 TCTCTTCCTAAATAACATGGTATCAAAACAGTTTTGGCAGATCTATTTCCTTTGAAACAGAGTTC
5916873 TTAT
196 TTAT
* *
5916877 TTATAGAGATT-GGTAATTATCATAATTGTAGGGA-TTTTATTTTCTTTATTTTCTTTATTCTTT
1 TTATAGAAATTAGG-AATCATCATAATTGTAGGGATTTTTATTTTCTTTATTTTCTTTATTCTTT
*
5916940 TTCTATTTTAGAAATGTGTAGGCTGTATATATAGGTGATTTATTATGAATAAAAGGTGTGAAGTA
65 TTCTATTTTAGAAATGTGTAGGCTATATATATAGGTGATTTATTATGAATAAAAGGTGTGAAGT-
*
5917005 TTT-TCTTCCTAAATAACATGGTATCAAAACAGTTTTGGCAGATCTATTTCCTTTGAAATAGAGT
129 TTTCTCTTCCTAAATAACATGGTATCAAAACAGTTTTGGCAGATCTATTTCCTTTGAAACAGAGT
5917069 TCTTA
194 TCTTA
5917074 GTTCTTCTTT
Statistics
Matches: 184, Mismatches: 11, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
198 152 0.83
199 32 0.17
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (199 bp):
TTATAGAAATTAGGAATCATCATAATTGTAGGGATTTTTATTTTCTTTATTTTCTTTATTCTTTT
TCTATTTTAGAAATGTGTAGGCTATATATATAGGTGATTTATTATGAATAAAAGGTGTGAAGTTT
TCTCTTCCTAAATAACATGGTATCAAAACAGTTTTGGCAGATCTATTTCCTTTGAAACAGAGTTC
TTAT
Found at i:5920516 original size:25 final size:24
Alignment explanation
Indices: 5920488--5920576 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 24
5920478 TTAATAAACG
5920488 TAATTATAGAAATTAGAAATCACCA
1 TAATTATAGAAATT-GAAATCACCA
* **
5920513 TAATTACAGGGATTGAAAATCACCA
1 TAATTATAGAAATTG-AAATCACCA
* ** * *
5920538 CAATTATAGGGATTGGGAATCATCA
1 TAATTATAGAAATT-GAAATCACCA
*
5920563 TAATTGTAGAAATT
1 TAATTATAGAAATT
5920577 TTATTTTTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 1 0.02
25 49 0.96
26 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (24 bp):
TAATTATAGAAATTGAAATCACCA
Found at i:5921781 original size:10 final size:10
Alignment explanation
Indices: 5921763--5921806 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
5921753 TACAAATGTG
* *
5921763 TATATATATT
1 TATACATATA
5921773 TATACATATA
1 TATACATATA
*
5921783 TATACATACA
1 TATACATATA
*
5921793 TATACACATA
1 TATACATATA
5921803 TATA
1 TATA
5921807 TAATGCTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (10 bp):
TATACATATA
Found at i:5926380 original size:14 final size:14
Alignment explanation
Indices: 5926363--5926393 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5926353 TCCAAGCTCG
*
5926363 TTTGTCTTTTAGTA
1 TTTGTCTTATAGTA
5926377 TTTGTCTTATAGTA
1 TTTGTCTTATAGTA
5926391 TTT
1 TTT
5926394 TTAGCATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTGTCTTATAGTA
Found at i:5933826 original size:21 final size:18
Alignment explanation
Indices: 5933801--5933848 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
5933791 ACATTTTATG
5933801 AAAATATATTAATTTTTAAA
1 AAAATAT-TTAA-TTTTAAA
*
5933821 ATAAATATTTTATTTTAAA
1 A-AAATATTTAATTTTAAA
5933840 AAAATATTT
1 AAAATATTT
5933849 TTTATTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 8 0.31
20 4 0.15
21 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAATATTTAATTTTAAA
Found at i:5933828 original size:19 final size:18
Alignment explanation
Indices: 5933801--5933847 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
5933791 ACATTTTATG
*
5933801 AAAATATATTA-ATTTTTA
1 AAAAAATATTATA-TTTTA
*
5933819 AAATAAATATTTTATTTTA
1 AAA-AAATATTATATTTTA
5933838 AAAAAATATT
1 AAAAAATATT
5933848 TTTTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 10 0.40
19 14 0.56
20 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAAAATATTATATTTTA
Found at i:5933854 original size:20 final size:19
Alignment explanation
Indices: 5933814--5933849 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5933804 ATATATTAAT
5933814 TTTTAAAATAAATATTTTA
1 TTTTAAAATAAATATTTTA
5933833 TTTTAAAA-AAATATTTT
1 TTTTAAAATAAATATTTT
5933850 TTATTATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAATAAATATTTTA
Found at i:5936247 original size:12 final size:12
Alignment explanation
Indices: 5936230--5936271 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
5936220 GTCTGTAGTA
*
5936230 TATATATATATG
1 TATATATGTATG
5936242 TATATATGTATG
1 TATATATGTATG
5936254 TATATATGTATG
1 TATATATGTATG
*
5936266 CATATA
1 TATATA
5936272 AAAATAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (12 bp):
TATATATGTATG
Found at i:5946884 original size:20 final size:21
Alignment explanation
Indices: 5946856--5946894 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
5946846 GGTTTCTTGT
5946856 GGTGTTTTTTTGACACTTGGG
1 GGTGTTTTTTTGACACTTGGG
5946877 GGTG-TTTTTTGACACTTG
1 GGTGTTTTTTTGACACTTG
5946895 CTGAGTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.10, G:0.31, T:0.49
Consensus pattern (21 bp):
GGTGTTTTTTTGACACTTGGG
Found at i:5956164 original size:38 final size:38
Alignment explanation
Indices: 5956119--5956194 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
5956109 GCATTGATGT
*
5956119 GGATTTTATAAGTAGTGATATAAAATTGTCTAATGTGA
1 GGATTTTATAAGTAGTGACATAAAATTGTCTAATGTGA
* * * *
5956157 GGATTTTATGAGTATTGACATGAAATTGTTTAATGTGA
1 GGATTTTATAAGTAGTGACATAAAATTGTCTAATGTGA
5956195 AGTTATCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.41
Consensus pattern (38 bp):
GGATTTTATAAGTAGTGACATAAAATTGTCTAATGTGA
Found at i:5957012 original size:28 final size:28
Alignment explanation
Indices: 5956942--5957013 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
5956932 TATAAAGAAG
* *
5956942 AGGTATAAATAAAAAGTTATATGAAAAC
1 AGGTATAAAAAAAAAGGTATATGAAAAC
* * *
5956970 AAGT-TAAAAGGAAAAGGTATATGTAAAC
1 AGGTATAAAA-AAAAAGGTATATGAAAAC
5956998 AGGTATAAAAAAAAAG
1 AGGTATAAAAAAAAAG
5957014 ATGTAAGTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
27 4 0.11
28 26 0.74
29 5 0.14
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (28 bp):
AGGTATAAAAAAAAAGGTATATGAAAAC
Found at i:5962975 original size:10 final size:10
Alignment explanation
Indices: 5962960--5963003 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
5962950 CTATCACATG
5962960 ATATACATAT
1 ATATACATAT
*
5962970 ATATACATCT
1 ATATACATAT
*
5962980 ATATGCATAT
1 ATATACATAT
5962990 ATATGA-ATAT
1 ATAT-ACATAT
5963000 ATAT
1 ATAT
5963004 TTTGTAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (10 bp):
ATATACATAT
Found at i:5963479 original size:23 final size:23
Alignment explanation
Indices: 5963448--5963499 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5963438 AGTTTTTTTA
5963448 TTATATTTAAATAAATATAAATTT
1 TTATATTTAAATAAATA-AAATTT
*
5963472 TTAT-TTTAATTAAAT-AAATTT
1 TTATATTTAAATAAATAAAATTT
*
5963493 TTTTATT
1 TTATATT
5963500 AACTATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 9 0.36
22 2 0.08
23 10 0.40
24 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATTTAAATAAATAAAATTT
Found at i:5964278 original size:13 final size:14
Alignment explanation
Indices: 5964259--5964291 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5964249 AAACAATTAG
*
5964259 TTTTTTTTTTTAAA
1 TTTTTTGTTTTAAA
5964273 TTTTTTGTTTTAAA
1 TTTTTTGTTTTAAA
5964287 TTTTT
1 TTTTT
5964292 ATAATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTTTGTTTTAAA
Found at i:5965231 original size:26 final size:24
Alignment explanation
Indices: 5965202--5965253 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
5965192 ATAAATACTT
*
5965202 ATATAAACAACAACAAATAATTAAAA
1 ATATAAACAAAAAC-AATAA-TAAAA
*
5965228 ATATAAATAAAAACAATAATAAAA
1 ATATAAACAAAAACAATAATAAAA
5965252 AT
1 AT
5965254 TTTTGAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 5 0.21
26 12 0.50
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (24 bp):
ATATAAACAAAAACAATAATAAAA
Found at i:5979116 original size:6 final size:6
Alignment explanation
Indices: 5979105--5979129 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5979095 ATTCAGGAAC
5979105 GGAATA GGAATA GGAATA GGAATA G
1 GGAATA GGAATA GGAATA GGAATA G
5979130 TTAAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GGAATA
Found at i:5979298 original size:41 final size:41
Alignment explanation
Indices: 5979241--5979321 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
5979231 GACTAGCATT
5979241 GTCAGTACCCAATCCAGGGACAGGTAATTCGAGGATTCTTA
1 GTCAGTACCCAATCCAGGGACAGGTAATTCGAGGATTCTTA
5979282 GTCAGTACCCAATCCAGGGACAGGTAATTCGAGGATTCTT
1 GTCAGTACCCAATCCAGGGACAGGTAATTCGAGGATTCTT
5979322 CTCTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (41 bp):
GTCAGTACCCAATCCAGGGACAGGTAATTCGAGGATTCTTA
Found at i:5987256 original size:18 final size:18
Alignment explanation
Indices: 5987229--5987263 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
5987219 AATTATGCAA
5987229 TATAATATAATAATTTTAC
1 TATAATATAAT-ATTTTAC
5987248 TATAA-ATAATATTTTA
1 TATAATATAATATTTTA
5987264 AGTGATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATATAATATTTTAC
Found at i:5988437 original size:18 final size:20
Alignment explanation
Indices: 5988396--5988437 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5988386 CTTACTTACT
* *
5988396 ATATTTTTTATAACTATCTT
1 ATATTTTTTATAACTAACTA
5988416 ATATTTTTTA-AA-TAACTA
1 ATATTTTTTATAACTAACTA
5988434 ATAT
1 ATAT
5988438 AAAATTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 10 0.50
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTTTATAACTAACTA
Found at i:5989036 original size:20 final size:21
Alignment explanation
Indices: 5989000--5989038 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5988990 TTAATTTTTA
*
5989000 TATATTTTTAGTAAAATTAAT
1 TATATTATTAGTAAAATTAAT
5989021 TATATTATTA-TAAAATTA
1 TATATTATTAGTAAAATTA
5989039 TATAATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TATATTATTAGTAAAATTAAT
Found at i:5990418 original size:79 final size:79
Alignment explanation
Indices: 5990281--5990440 Score: 275
Period size: 79 Copynumber: 2.0 Consensus size: 79
5990271 ATATAAACAC
* *
5990281 TTACGCACTTTATAGGTCTAAGAAACTATGACATCGATCACATGAAAATAGCTTAATCAAGGCAT
1 TTACCCACTTTATAGGTCTAAGAAACTATGACATCGATCACATGAAAATAGCTCAATCAAGGCAT
5990346 TGAAATTTGATAGT
66 TGAAATTTGATAGT
* * *
5990360 TTACCCACTTTATAGGTCTAAGAAACTTTGACATTGATCACATGAGAATAGCTCAATCAAGGCAT
1 TTACCCACTTTATAGGTCTAAGAAACTATGACATCGATCACATGAAAATAGCTCAATCAAGGCAT
5990425 TGAAATTTGATAGT
66 TGAAATTTGATAGT
5990439 TT
1 TT
5990441 CAAGTTGTGG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (79 bp):
TTACCCACTTTATAGGTCTAAGAAACTATGACATCGATCACATGAAAATAGCTCAATCAAGGCAT
TGAAATTTGATAGT
Found at i:5994019 original size:22 final size:21
Alignment explanation
Indices: 5993971--5994019 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
5993961 ATATTTAAAC
5993971 TTAAAAAATAAAACAT-AAAA
1 TTAAAAAATAAAACATAAAAA
*
5993991 TTATAAAGAATAAAATATAAATAA
1 TTA-AAA-AATAAAACATAAA-AA
5994015 TTAAA
1 TTAAA
5994020 TACGAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 3 0.12
22 9 0.38
23 4 0.17
24 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TTAAAAAATAAAACATAAAAA
Found at i:5994244 original size:27 final size:27
Alignment explanation
Indices: 5994201--5994253 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5994191 GTTAGTTACT
*
5994201 AGAAAAGAGAAATGAAAATAAAAAGAC
1 AGAAAAGAGAAATGAAAAAAAAAAGAC
5994228 AGAAAAGAGAAGA-GAAAAAAAAAAGA
1 AGAAAAGAGAA-ATGAAAAAAAAAAGA
5994254 GAAAGAGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.04
Consensus pattern (27 bp):
AGAAAAGAGAAATGAAAAAAAAAAGAC
Found at i:5994485 original size:12 final size:12
Alignment explanation
Indices: 5994468--5994493 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5994458 ACCGTCCGCC
5994468 CCTGTTCAATTT
1 CCTGTTCAATTT
5994480 CCTGTTCAATTT
1 CCTGTTCAATTT
5994492 CC
1 CC
5994494 ATCTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (12 bp):
CCTGTTCAATTT
Found at i:6007120 original size:21 final size:21
Alignment explanation
Indices: 6007094--6007136 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6007084 ACTATTGCAC
6007094 TTGGTCATGGAAGGAAAGCAG
1 TTGGTCATGGAAGGAAAGCAG
6007115 TTGGTCATGGAAGGAAAGCAG
1 TTGGTCATGGAAGGAAAGCAG
6007136 T
1 T
6007137 AAGTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.37, T:0.21
Consensus pattern (21 bp):
TTGGTCATGGAAGGAAAGCAG
Found at i:6014322 original size:154 final size:155
Alignment explanation
Indices: 6014042--6014356 Score: 481
Period size: 154 Copynumber: 2.0 Consensus size: 155
6014032 TTTATGTAGT
* *
6014042 ATAACCAGTCCATCTTCTAGTTTCTTTTGTGATAATGCTATTGATAAGCCTCTATAATTCTAGGG
1 ATAACCAGTCCATCTTCTAGTTTCTTTTGTGATAATGCTATAGATAAGCCTCTATAATTCTAGAG
*
6014107 TCAATATCCAATTAATTCAACTCCTAGAAGCAATGCATTTGTTGGATGAATTCTCAACATGG-TG
66 TCAATATCCAATTAATTCAACTCCTAGAAGCAATGCATTTGTTGGATGAAATCTCAACATGGCTG
* **
6014171 ATGCCAATTGATTACTTGGTTCATG
131 ATACCAATTGATTACTCAGTTCATG
* *
6014196 ATAACCAGTCCATCTTGTAGTTTCTTTTGTGATATCTGCTATAGAT-AGCCTCTATAATTCTAGA
1 ATAACCAGTCCATCTTCTAGTTTCTTTTGTGATA-ATGCTATAGATAAGCCTCTATAATTCTAGA
* * *
6014260 GTCGATATCCAATTGATTCAACTCCTGGAAGCAATGCATTTGTTGGATGAAATCTCAACATGGTC
65 GTCAATATCCAATTAATTCAACTCCTAGAAGCAATGCATTTGTTGGATGAAATCTCAACATGG-C
**
6014325 TGATACCCTTTGATTACTCAGTTCATG
129 TGATACCAATTGATTACTCAGTTCATG
6014352 ATAAC
1 ATAAC
6014357 TTTACGAATT
Statistics
Matches: 145, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
154 109 0.75
155 9 0.06
156 27 0.19
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (155 bp):
ATAACCAGTCCATCTTCTAGTTTCTTTTGTGATAATGCTATAGATAAGCCTCTATAATTCTAGAG
TCAATATCCAATTAATTCAACTCCTAGAAGCAATGCATTTGTTGGATGAAATCTCAACATGGCTG
ATACCAATTGATTACTCAGTTCATG
Found at i:6039891 original size:2 final size:2
Alignment explanation
Indices: 6039884--6039908 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6039874 GACTCAATAG
6039884 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
6039909 ACACACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6039913 original size:2 final size:2
Alignment explanation
Indices: 6039908--6039936 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6039898 CTCTCTCTCT
6039908 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
6039937 TAATACCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6053498 original size:16 final size:17
Alignment explanation
Indices: 6053477--6053509 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6053467 TTTTTTCCTC
6053477 TTCTC-TTTTATTTTTT
1 TTCTCTTTTTATTTTTT
6053493 TTCTCTTTTTATTTTTT
1 TTCTCTTTTTATTTTTT
6053510 ATTTTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TTCTCTTTTTATTTTTT
Found at i:6054173 original size:39 final size:40
Alignment explanation
Indices: 6054130--6054212 Score: 116
Period size: 39 Copynumber: 2.1 Consensus size: 40
6054120 TTATACAACA
*
6054130 AAAAGGTTTTATTTACAAAAATTGCTCATTT-AGGCTAA-G
1 AAAAGGTTTCATTTACAAAAATTGCTCATTTCA-GCTAAGG
* *
6054169 AAAAGGTTTCATTTATAGAAATTGCTCATTTCAGCTAAGG
1 AAAAGGTTTCATTTACAAAAATTGCTCATTTCAGCTAAGG
6054209 AAAA
1 AAAA
6054213 TGACCTTGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 33 0.85
40 6 0.15
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (40 bp):
AAAAGGTTTCATTTACAAAAATTGCTCATTTCAGCTAAGG
Found at i:6062702 original size:36 final size:37
Alignment explanation
Indices: 6062662--6062759 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 37
6062652 AAAGCAGGAA
*
6062662 AGGTCGGGACTCGCAGGAGGGGGGTCGG-GGGAAATC
1 AGGTCGGGACTCGCAGGAGGGGGGGCGGCGGGAAATC
* * * *
6062698 AGGTCTGGACTCGCTGGAGGGGGGGGGGCGGGGAATC
1 AGGTCGGGACTCGCAGGAGGGGGGGCGGCGGGAAATC
* *
6062735 AGGTCGAGATTCG-AGGGAGGGGGGG
1 AGGTCGGGACTCGCA-GGAGGGGGGG
6062760 AAGGAGTTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
36 24 0.47
37 27 0.53
ACGTcount: A:0.17, C:0.14, G:0.56, T:0.12
Consensus pattern (37 bp):
AGGTCGGGACTCGCAGGAGGGGGGGCGGCGGGAAATC
Found at i:6076723 original size:23 final size:22
Alignment explanation
Indices: 6076667--6076723 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
6076657 TAAATTAATT
* *
6076667 ATTAATTATTATGATTAATATA
1 ATTAATTATTATTATAAATATA
*
6076689 A--AAATATTATTATAAATATA
1 ATTAATTATTATTATAAATATA
6076709 ATTAATTATTGATTA
1 ATTAATTATT-ATTA
6076724 ATTGGATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 17 0.61
22 7 0.25
23 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTAATTATTATTATAAATATA
Found at i:6080846 original size:2 final size:2
Alignment explanation
Indices: 6080839--6080870 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6080829 AACTAGAGTG
6080839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6080871 CAATTAGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6088574 original size:2 final size:2
Alignment explanation
Indices: 6088561--6088591 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6088551 GCAAAAGACC
*
6088561 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6088592 CAGAAGACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6097264 original size:16 final size:15
Alignment explanation
Indices: 6097245--6097274 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6097235 AAATCATTAA
6097245 ATTTATAAAATAATAT
1 ATTTATAAAA-AATAT
6097261 ATTTATAAAAAATA
1 ATTTATAAAAAATA
6097275 CATATATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTATAAAAAATAT
Found at i:6104832 original size:3 final size:3
Alignment explanation
Indices: 6104826--6104853 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6104816 GTCTCTTCTT
6104826 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
6104854 GCTACTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:6110107 original size:11 final size:10
Alignment explanation
Indices: 6110090--6110114 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6110080 GAATAATTCC
6110090 CTTTTTTTTT
1 CTTTTTTTTT
6110100 CTTTTTTTTT
1 CTTTTTTTTT
6110110 CTTTT
1 CTTTT
6110115 AAGAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:6110934 original size:5 final size:5
Alignment explanation
Indices: 6110924--6110954 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
6110914 CACATATTCA
6110924 TTATT TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT T
6110955 GGGTTGGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:6113769 original size:21 final size:20
Alignment explanation
Indices: 6113745--6113784 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6113735 AATTATATAA
*
6113745 AGATATATTAATTTTTAAAAC
1 AGATAT-TTAATTTTAAAAAC
*
6113766 AGATATTTTATTTTAAAAA
1 AGATATTTAATTTTAAAAA
6113785 AATATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
AGATATTTAATTTTAAAAAC
Found at i:6113793 original size:19 final size:19
Alignment explanation
Indices: 6113757--6113792 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6113747 ATATATTAAT
*
6113757 TTTTAAAACAGATATTTTA
1 TTTTAAAACAAATATTTTA
6113776 TTTTAAAA-AAATATTTT
1 TTTTAAAACAAATATTTT
6113793 TCATTAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTAAAACAAATATTTTA
Found at i:6123808 original size:2 final size:2
Alignment explanation
Indices: 6123795--6123826 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6123785 ACTAACAGGG
*
6123795 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6123827 GACGTGATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.