Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 31
Found at i:3694741 original size:64 final size:63
Alignment explanation
Indices: 3694659--3694815 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 63
3694649 TTCAGTGTGT
* * *
3694659 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGCAATTAGTGC
* ** * *
3694723 ATCGATGCATAAGG-AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
* * *
3694787 ATTGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
3694816 ATGTTAAAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
63 3 0.04
64 69 0.86
65 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:3694848 original size:20 final size:20
Alignment explanation
Indices: 3694803--3694860 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
3694793 GCATGGGTAG
3694803 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
3694827 TGCATTGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
3694847 TGTATCGATGCACT
1 TGCATCGATGCACT
3694861 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:3696377 original size:23 final size:23
Alignment explanation
Indices: 3696351--3696410 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
3696341 ATGGCACTTT
3696351 GGTGCATTTCTACGCGGCACTAC
1 GGTGCATTTCTACGCGGCACTAC
* * ** *
3696374 GGTGTAATTCTACGTTGCACTTC
1 GGTGCATTTCTACGCGGCACTAC
*
3696397 GGTGCATTTATACG
1 GGTGCATTTCTACG
3696411 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.33
Consensus pattern (23 bp):
GGTGCATTTCTACGCGGCACTAC
Found at i:3697319 original size:21 final size:21
Alignment explanation
Indices: 3697290--3697366 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3697280 TGCAAGAAAT
* *
3697290 GGATTGATCATTTTCATCGAG
1 GGATCGATCCTTTTCATCGAG
* *
3697311 GGATCGATCCTTTTCCTCAAG
1 GGATCGATCCTTTTCATCGAG
*
3697332 GGATCGATCCTTGTCATCGAG
1 GGATCGATCCTTTTCATCGAG
3697353 GGATCGATCCTTTT
1 GGATCGATCCTTTT
3697367 GTGAAATGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.35
Consensus pattern (21 bp):
GGATCGATCCTTTTCATCGAG
Found at i:3697427 original size:20 final size:20
Alignment explanation
Indices: 3697398--3697435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3697388 TTTCTAAAAT
3697398 CCAAGGGATCAATCCTTTTA
1 CCAAGGGATCAATCCTTTTA
* *
3697418 CCAAGTGATCGATCCTTT
1 CCAAGGGATCAATCCTTT
3697436 AAACCAAAAA
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:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (20 bp):
CCAAGGGATCAATCCTTTTA
Found at i:3697973 original size:43 final size:43
Alignment explanation
Indices: 3697913--3698010 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
3697903 CTTTTCTTTT
* * * *
3697913 GTGGTGTTTTGTCCCAAAAATGTCGCTAAATTTTCTAACATATA
1 GTGGTG-TTTGTCCCAAAAACGCCGCTAAATGTTATAACATATA
* **
3697957 GTGGTGTTTGTTCCAAAAACGCCGCTAAATGTTATGTCATATA
1 GTGGTGTTTGTCCCAAAAACGCCGCTAAATGTTATAACATATA
*
3698000 GTGGCGTTTGT
1 GTGGTGTTTGT
3698011 GAATGTAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 40 0.87
44 6 0.13
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (43 bp):
GTGGTGTTTGTCCCAAAAACGCCGCTAAATGTTATAACATATA
Found at i:3698198 original size:16 final size:16
Alignment explanation
Indices: 3698177--3698207 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3698167 GCAAATGCTG
*
3698177 CTTTCTGGAATCCAAA
1 CTTTCTAGAATCCAAA
3698193 CTTTCTAGAATCCAA
1 CTTTCTAGAATCCAA
3698208 GGGATCGATC
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:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (16 bp):
CTTTCTAGAATCCAAA
Found at i:3698947 original size:16 final size:16
Alignment explanation
Indices: 3698926--3698965 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3698916 ATTGAATCAG
*
3698926 AAGCAACCCAAACCGA
1 AAGCAACCCAAACCAA
* *
3698942 AAGCAACTCGAACCAA
1 AAGCAACCCAAACCAA
3698958 AAGCAACC
1 AAGCAACC
3698966 TGGATCGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.12, T:0.03
Consensus pattern (16 bp):
AAGCAACCCAAACCAA
Found at i:3699689 original size:14 final size:15
Alignment explanation
Indices: 3699670--3699711 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
3699660 AATCTACCCC
*
3699670 TATATTATTATTAT-
1 TATATTTTTATTATA
3699684 TATATTTTTATTATA
1 TATATTTTTATTATA
*
3699699 AATATTTTTATTA
1 TATATTTTTATTA
3699712 AACAAACTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTTTTATTATA
Found at i:3699819 original size:23 final size:23
Alignment explanation
Indices: 3699789--3699833 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3699779 AAACAAAAAC
*
3699789 ACCCAAA-CAGAACCCGACCCGAG
1 ACCCAAACCA-AACCCAACCCGAG
3699812 ACCCAAACCAAACCCAACCCGA
1 ACCCAAACCAAACCCAACCCGA
3699834 ACCAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.42, C:0.47, G:0.11, T:0.00
Consensus pattern (23 bp):
ACCCAAACCAAACCCAACCCGAG
Found at i:3700721 original size:31 final size:30
Alignment explanation
Indices: 3700683--3700743 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
3700673 CAATTTAAGG
*
3700683 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTT-AATTAAATTTA
3700714 CAAAATGGTTTTTGGACTTAATTAAATTTA
1 CAAAATGGTTTTTGGACTTAATTAAATTTA
3700744 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (30 bp):
CAAAATGGTTTTTGGACTTAATTAAATTTA
Found at i:3700894 original size:22 final size:21
Alignment explanation
Indices: 3700823--3700880 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
3700813 AGGGTGTCAA
* *
3700823 AGTGCATCCATACACCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
3700844 AGTGCTTCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
3700865 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
3700881 TGCACTAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:3700967 original size:20 final size:20
Alignment explanation
Indices: 3700942--3701015 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
3700932 AAAGCAATTA
3700942 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
***
3700962 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTTCT
3700983 GTGCATCGATGCATCCTGT-T
1 GTGCATCGATGCATCCT-TCT
*
3701003 GTGCATCTATGCA
1 GTGCATCGATGCA
3701016 CGAAGGCTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:3700986 original size:21 final size:20
Alignment explanation
Indices: 3700942--3700997 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
3700932 AAAGCAATTA
***
3700942 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGGCT
3700962 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-AGGCT
3700983 GTGCATCGATGCATC
1 GTGCATCGATGCATC
3700998 CTGTTGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGCT
Found at i:3700999 original size:41 final size:41
Alignment explanation
Indices: 3700942--3701024 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
3700932 AAAGCAATTA
3700942 GTGCATCGATGCATCCT-TCTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCATCCTGT-TGTGCATCGATGCA-CGAAGGCT
*
3700983 GTGCATCGATGCATCCTGTTGTGCATCTATGCACGAAGGCT
1 GTGCATCGATGCATCCTGTTGTGCATCGATGCACGAAGGCT
3701024 G
1 G
3701025 CAACGGTTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 1 0.03
41 37 0.95
42 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGTTGTGCATCGATGCACGAAGGCT
Found at i:3704324 original size:30 final size:31
Alignment explanation
Indices: 3704268--3704328 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3704258 CAATTTAAGG
3704268 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
3704299 CAAAATGGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
3704329 TTCAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:3704437 original size:21 final size:21
Alignment explanation
Indices: 3704408--3704527 Score: 125
Period size: 21 Copynumber: 5.7 Consensus size: 21
3704398 AGGGTGTCAA
*
3704408 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCATGC
* *
3704429 AGTGTATCCATGCATCCATGC
1 AGTGCATCCATGCACCCATGC
*
3704450 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCACCCATGC
** **
3704471 AGTGCATCCATGCACCTGTAAT
1 AGTGCATCCATGCACCCAT-GC
* * *
3704493 AGTGAATCGATGCA-TCATGC
1 AGTGCATCCATGCACCCATGC
3704513 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3704528 TCAAACACCA
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 12 0.15
21 55 0.70
22 12 0.15
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:3704455 original size:13 final size:13
Alignment explanation
Indices: 3704439--3704484 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
3704429 AGTGTATCCA
3704439 TGCATCCATGCAG
1 TGCATCCATGCAG
3704452 TGCAT-C---CA-
1 TGCATCCATGCAG
3704460 TGCATCCATGCAG
1 TGCATCCATGCAG
3704473 TGCATCCATGCA
1 TGCATCCATGCA
3704485 CCTGTAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 5 0.18
9 3 0.11
12 3 0.11
13 17 0.61
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:3706198 original size:2 final size:2
Alignment explanation
Indices: 3706191--3706281 Score: 164
Period size: 2 Copynumber: 45.5 Consensus size: 2
3706181 ATTAATTATG
3706191 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
*
3706233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3706275 TG TA TA T
1 TA TA TA T
3706282 TATTTGCATA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3707347 original size:391 final size:391
Alignment explanation
Indices: 3706638--3707801 Score: 2082
Period size: 391 Copynumber: 3.0 Consensus size: 391
3706628 TAATTTTTAA
* * *
3706638 ATTTAGGTGAATTCTTAATTTGGTTCTCGCTTTTTATCGAGGTTCTGAATTAATTATTCGAATCA
1 ATTTAGGCGAATTCTTAATTTGGTTCTCGCTTTTGATCGAGGTTCCGAATTAATTATTCGAATCA
3706703 CACAAATAATTAAAATTGAATAGGTTAATATTTTAGAGCCTTTA-TT---G--------CAAACT
66 CACAAATAATTAAAATTGAATAGGTTAATATTTTAGAGCCTTTATTTCAAGCTTAATTTCAAACT
3706756 TAGTCCTTTAATTTGGGAATTAATCTGAGTTGGCCCTCACATAAATGCTCAAGGGACCATCTCGA
131 TAGTCCTTTAATTTGGGAATTAATCTGAGTTGGCCCTCACATAAATGCTCAAGGGACCATCTCGA
3706821 TTATTAGATTCAATAATTGATTTAAAATCAAATAAGGTTAATATTAGAACCTACATTTTAGGCTT
196 TTATTAGATTCAATAATTGATTTAAAATCAAATAAGGTTAATATTAGAACCTACATTTTAGGCTT
3706886 GAGCTTCTAGGTTCCCTAATTTTCATAATTTGACATTTTAAGCTAGAAAAAGCCTTAATTCACCC
261 GAGCTTCTAGGTTCCCTAATTTTCATAATTTGACATTTTAAGCTAGAAAAAGCCTTAATTCACCC
*
3706951 TTAATTAGGATGAATAAAAATTTGCTTGATTGCATTTTATTTTTAAACCTAAGGCAATATTCACT
326 TTAATTAGGATGAATAAAAATTTGCTTGATTGCATTTTATTTTTAAACCTAAGGCAATGTTCACT
3707016 T
391 T
* * *
3707017 ATTTAGGCGAATTCTTAATTTGGTTCTCACTTTTGACCGAGGTTCCGAATTAATTATTCAAATCA
1 ATTTAGGCGAATTCTTAATTTGGTTCTCGCTTTTGATCGAGGTTCCGAATTAATTATTCGAATCA
*
3707082 CACAAATAATTAAAATTGAATATGTTAATATTTTAGAGCCTTTATTTCAAGCTTAATTTCAAACT
66 CACAAATAATTAAAATTGAATAGGTTAATATTTTAGAGCCTTTATTTCAAGCTTAATTTCAAACT
*
3707147 TAGTCCTTTAATTTGTGAATTAATCTGAGTTGGCCCTCACATAAATGCTCAAGGGACCATCTCGA
131 TAGTCCTTTAATTTGGGAATTAATCTGAGTTGGCCCTCACATAAATGCTCAAGGGACCATCTCGA
*
3707212 TTATTCGATTCAATAATTGATTTAAAATCAAATAAGGTTAATATTAGAACCTACATTTTAGGCTT
196 TTATTAGATTCAATAATTGATTTAAAATCAAATAAGGTTAATATTAGAACCTACATTTTAGGCTT
3707277 GAGCTTCTAGGTTCCCTAATTTTCATAATTTGACATTTTAAGCTAGAAAAAGCCTTAATTCACCC
261 GAGCTTCTAGGTTCCCTAATTTTCATAATTTGACATTTTAAGCTAGAAAAAGCCTTAATTCACCC
3707342 TTAATTAGGATGAATAAAAATTTGCTTGATTGCATTTTATTTTTAAACCTAAGGCAATGTTCACT
326 TTAATTAGGATGAATAAAAATTTGCTTGATTGCATTTTATTTTTAAACCTAAGGCAATGTTCACT
3707407 T
391 T
* * *
3707408 ATTTAGGCAAATTCTTAATTTGGTTCTCGCTTTTGGTCGAAGTTCCGAATTAATTATTCGAATCA
1 ATTTAGGCGAATTCTTAATTTGGTTCTCGCTTTTGATCGAGGTTCCGAATTAATTATTCGAATCA
*
3707473 CACAAATAATTAAAATTGAATAGGTTCATATTTTAGAGCCTTTATTTCAAGCTTAATTTCAAACT
66 CACAAATAATTAAAATTGAATAGGTTAATATTTTAGAGCCTTTATTTCAAGCTTAATTTCAAACT
** *
3707538 TAGTCCTTTAATTTGGGAATTAATCTGAGTTGGCCCTCACATAAATGCTCAAATGATCATCTCGA
131 TAGTCCTTTAATTTGGGAATTAATCTGAGTTGGCCCTCACATAAATGCTCAAGGGACCATCTCGA
3707603 TTATTAGATTCAATAATTGATTTAAAATCAAATAAGGTTAATATTAGAACCTACATTTTAGGCTT
196 TTATTAGATTCAATAATTGATTTAAAATCAAATAAGGTTAATATTAGAACCTACATTTTAGGCTT
3707668 GAGCTTCTAGGTTCCCTAATTTTCATAATTTGACATTTTAAGCTAGAAAAAGCCTTAATTCACCC
261 GAGCTTCTAGGTTCCCTAATTTTCATAATTTGACATTTTAAGCTAGAAAAAGCCTTAATTCACCC
*
3707733 TTAATTAGGATGAATAAAACTTTGCTTGATTGCATTTTATTTTTAAACCTAAGGCAATGTTCACT
326 TTAATTAGGATGAATAAAAATTTGCTTGATTGCATTTTATTTTTAAACCTAAGGCAATGTTCACT
3707798 T
391 T
3707799 ATT
1 ATT
3707802 AAGGAATTAA
Statistics
Matches: 749, Mismatches: 24, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
379 102 0.14
380 2 0.00
383 1 0.00
391 644 0.86
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (391 bp):
ATTTAGGCGAATTCTTAATTTGGTTCTCGCTTTTGATCGAGGTTCCGAATTAATTATTCGAATCA
CACAAATAATTAAAATTGAATAGGTTAATATTTTAGAGCCTTTATTTCAAGCTTAATTTCAAACT
TAGTCCTTTAATTTGGGAATTAATCTGAGTTGGCCCTCACATAAATGCTCAAGGGACCATCTCGA
TTATTAGATTCAATAATTGATTTAAAATCAAATAAGGTTAATATTAGAACCTACATTTTAGGCTT
GAGCTTCTAGGTTCCCTAATTTTCATAATTTGACATTTTAAGCTAGAAAAAGCCTTAATTCACCC
TTAATTAGGATGAATAAAAATTTGCTTGATTGCATTTTATTTTTAAACCTAAGGCAATGTTCACT
T
Found at i:3708877 original size:31 final size:31
Alignment explanation
Indices: 3708850--3708963 Score: 201
Period size: 31 Copynumber: 3.7 Consensus size: 31
3708840 ATGTTTTCTC
* *
3708850 CGTTATACTTTTAGGTGCCTAACGTTTTTTA
1 CGTTACACTTTTAGGTGTCTAACGTTTTTTA
3708881 CGTTACACTTTTAGGTGTCTAACGTTTTTTA
1 CGTTACACTTTTAGGTGTCTAACGTTTTTTA
3708912 CGTTACACTTTTAGGTGTCTAACGTTTTTTA
1 CGTTACACTTTTAGGTGTCTAACGTTTTTTA
*
3708943 CATTACACTTTTAGGTGTCTA
1 CGTTACACTTTTAGGTGTCTA
3708964 TACAGTAACA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (31 bp):
CGTTACACTTTTAGGTGTCTAACGTTTTTTA
Found at i:3710898 original size:21 final size:22
Alignment explanation
Indices: 3710874--3710919 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3710864 GGAAAAGAAT
*
3710874 TGAAAG-GTTAAGAACTTTTGA
1 TGAAAGAGTTAAGAACATTTGA
*
3710895 TG-AAGAGTTAAGACCATTTGA
1 TGAAAGAGTTAAGAACATTTGA
3710916 TGAA
1 TGAA
3710920 GGTATTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 3 0.14
21 17 0.81
22 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (22 bp):
TGAAAGAGTTAAGAACATTTGA
Found at i:3710920 original size:21 final size:21
Alignment explanation
Indices: 3710880--3710920 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3710870 GAATTGAAAG
*
3710880 GTTAAGAACTTTTGATGAAGA
1 GTTAAGAACATTTGATGAAGA
*
3710901 GTTAAGACCATTTGATGAAG
1 GTTAAGAACATTTGATGAAG
3710921 GTATTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (21 bp):
GTTAAGAACATTTGATGAAGA
Found at i:3713660 original size:3 final size:3
Alignment explanation
Indices: 3713562--3713644 Score: 84
Period size: 3 Copynumber: 27.7 Consensus size: 3
3713552 TTTGGGTTTG
*
3713562 TAA TAA TAA CTTAA TTAA TAA TAA TAAA TAA TAA TAA TAA T-A TAA TAG
1 TAA TAA TAA --TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
3713610 TAA -AA TAA -AA TAA TAT TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3713645 TTATTATTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.12
3 51 0.74
4 7 0.10
5 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3714319 original size:123 final size:123
Alignment explanation
Indices: 3713963--3714326 Score: 581
Period size: 122 Copynumber: 3.0 Consensus size: 123
3713953 TACCTCCTTC
* * * * *
3713963 ATCTATATCTTTCTGTGGTAGAATCAAT-CAAAAGGTTGAACAATCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGT-AATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* *
3714027 TTTTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGTTG
65 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
* * *
3714086 ATCTATCTCCTTTTATGATAGAGTCATGC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTGTGATAGAGTAATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
*
3714150 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAATTTTCTCTGGAAAAGTTGATGTTG
66 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
3714208 ATCTATCTCCTTCTGTGATAGAGTAATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTGTGATAGAGTAATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
*
3714273 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TCTGGAAAAGTTGAT
66 TCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
3714327 CCATCGAATG
Statistics
Matches: 222, Mismatches: 16, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
122 117 0.53
123 75 0.34
124 30 0.14
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (123 bp):
ATCTATCTCCTTCTGTGATAGAGTAATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
Found at i:3714371 original size:113 final size:113
Alignment explanation
Indices: 3713992--3714543 Score: 544
Period size: 122 Copynumber: 4.7 Consensus size: 113
3713982 AGAATCAATC
* *
3713992 AAAAGGTTGAACAATCTCTTCTCATTATGAACTTCTTTTTCC-TCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
* ** * * *
3714056 TATGAACTTTCTCTGGAAAAATTGATGTTGATCTATCTCCTTTTATG-ATAGAGTCAT
66 TATGAACTTTCTCTGG--AAA---A-GTTGATCCA--T-CAATGATGAATTGAG-AAT
*
3714113 GCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCA
1 -AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
* * ** ** * *
3714177 TTATGAATTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTAAT
65 TTATGAACTTTCTCTGG-AAA----A-GTTGATCCATC-AATGATG-AATTGAG-AAT
*
3714235 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 --AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
*
3714300 ATTATGAACTTT-TCTGGAAAAGTTGATCCATCGAATGATGAATTCA-AAT
64 ATTATGAACTTTCTCTGGAAAAGTTGATCCATC-AATGATGAATTGAGAAT
** * * *
3714349 AAAAGGTTTGAACAAATTCTTCTCATTATGAATTTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
1 AAAAGG-TTGAACAAGCTCTTCTCATTATGAA-CTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * *
3714414 ATTATGAAC--TCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAGCA-
64 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAA-TGATGAA-TTGAGAAT
* *
3714463 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTCAT
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
3714528 TATGAACTTTCTCTGG
66 TATGAACTTTCTCTGG
3714544 CAATGGTAAT
Statistics
Matches: 382, Mismatches: 34, Indels: 36
0.85 0.08 0.08
Matches are distributed among these distances:
112 46 0.12
113 72 0.19
114 58 0.15
115 1 0.00
116 3 0.01
117 13 0.03
118 1 0.00
119 1 0.00
120 5 0.01
121 4 0.01
122 102 0.27
123 46 0.12
124 30 0.08
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (113 bp):
AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGTTGATCCATCAATGATGAATTGAGAAT
Found at i:3714407 original size:114 final size:113
Alignment explanation
Indices: 3714237--3714543 Score: 442
Period size: 113 Copynumber: 2.7 Consensus size: 113
3714227 AGAGTAATGC
*
3714237 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
3714302 TATGAACTTTTCTGGAAAAGTTGATCCATCGAA-TGATGAA-TTCA-AA
66 TATGAACTTTTCTGGAAAAGCTGATCCATC-AAGTGATGAATTTCAGAA
* * *
3714348 TAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 -AAAAGG-TTGAACAAGTTCTTCTCATTATGAA-CTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
3714413 CATTATGAAC-TCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAGCA
63 CATTATGAACTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTCAGAA
* *
3714463 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3714528 TATGAACTTTCTCTGG
66 TATGAACTTT-TCTGG
3714544 CAATGGTAAT
Statistics
Matches: 173, Mismatches: 15, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
112 45 0.26
113 74 0.43
114 53 0.31
115 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTCAGAA
Found at i:3715717 original size:18 final size:19
Alignment explanation
Indices: 3715689--3715766 Score: 79
Period size: 19 Copynumber: 3.9 Consensus size: 19
3715679 TTTACAAAAT
3715689 AAAAGAATAAATTGAATTTC
1 AAAA-AATAAATTGAATTTC
* *
3715709 -AAAAATAAATTAAATCTC
1 AAAAAATAAATTGAATTTC
3715727 AAAAAATAAATTGAATTT-
1 AAAAAATAAATTGAATTTC
3715745 AGAGAAAATAAACTTAGAATTT
1 A-A-AAAATAAA-TT-GAATTT
3715767 ATTAATAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 14 0.29
19 19 0.39
20 8 0.16
21 2 0.04
22 6 0.12
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTGAATTTC
Found at i:3716124 original size:9 final size:8
Alignment explanation
Indices: 3716098--3716187 Score: 101
Period size: 8 Copynumber: 11.0 Consensus size: 8
3716088 TTGACCCTTC
*
3716098 TTTTTATT
1 TTTTTCTT
*
3716106 TTCTTCTT
1 TTTTTCTT
3716114 TTTTTCTT
1 TTTTTCTT
*
3716122 TTTCTCCTT
1 TTT-TTCTT
3716131 TTTTTCTT
1 TTTTTCTT
3716139 TTTTTCTTT
1 TTTTTC-TT
3716148 TTTTTCTT
1 TTTTTCTT
3716156 TTTTTCTT
1 TTTTTCTT
*
3716164 TTTTT-TC
1 TTTTTCTT
*
3716171 TATTTCATT
1 TTTTTC-TT
3716180 TTTTTCTT
1 TTTTTCTT
3716188 CAAGCATAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
7 5 0.07
8 43 0.62
9 21 0.30
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3716124 original size:17 final size:16
Alignment explanation
Indices: 3716098--3716187 Score: 101
Period size: 17 Copynumber: 5.5 Consensus size: 16
3716088 TTGACCCTTC
* *
3716098 TTTTTATTTTCTTCTT
1 TTTTTCTTTTTTTCTT
*
3716114 TTTTTCTTTTTCTCCTT
1 TTTTTCTTTTT-TTCTT
3716131 TTTTTCTTTTTTTCTTT
1 TTTTTCTTTTTTTC-TT
3716148 TTTTTCTTTTTTTCTT
1 TTTTTCTTTTTTTCTT
* *
3716164 TTTTT-TCTATTTCATT
1 TTTTTCTTTTTTTC-TT
3716180 TTTTTCTT
1 TTTTTCTT
3716188 CAAGCATAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.10
16 25 0.40
17 32 0.51
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTTTTCTT
Found at i:3716138 original size:25 final size:25
Alignment explanation
Indices: 3716104--3716168 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
3716094 CTTCTTTTTA
*
3716104 TTTTCTTCTTTTTTTCTTTTTCTCC
1 TTTTTTTCTTTTTTTCTTTTTCTCC
* *
3716129 TTTTTTTCTTTTTTTCTTTTTTTTC
1 TTTTTTTCTTTTTTTCTTTTTCTCC
3716154 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTTTT
3716169 TCTATTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTTTTCTTTTTTTCTTTTTCTCC
Found at i:3726862 original size:20 final size:20
Alignment explanation
Indices: 3726819--3726862 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3726809 AAACATTAAT
* *
3726819 AAAATAATATAAATTTTATG
1 AAAATAATATAAATTATATA
3726839 AAAATAATA-AAATATATATA
1 AAAATAATATAAAT-TATATA
3726859 AAAA
1 AAAA
3726863 ATTTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAATAATATAAATTATATA
Found at i:3726872 original size:13 final size:13
Alignment explanation
Indices: 3726840--3726883 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3726830 AATTTTATGA
*
3726840 AAATAATAAAATAT
1 AAATAA-AAAATTT
*
3726854 ATATAAAAAATTT
1 AAATAAAAAATTT
3726867 AAATAAAAAA-TT
1 AAATAAAAAATTT
3726879 AAATA
1 AAATA
3726884 TATGAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 7 0.26
13 15 0.56
14 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAAAAATTT
Found at i:3729053 original size:33 final size:32
Alignment explanation
Indices: 3729013--3729095 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 32
3729003 TTTGTGTCTG
3729013 TAATAATAACT-TAAT-TAATAATAATAATAAAAA
1 TAATAATAA-TATAATATAA-AATAA-AATAAAAA
* *
3729046 TAATAATAATATAATAGTAAAATAAAATAATAT
1 TAATAATAATATAATA-TAAAATAAAATAAAAA
3729079 TAATAATAATATAATAT
1 TAATAATAATATAATAT
3729096 TATTATTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 2 0.04
33 35 0.78
34 5 0.11
35 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (32 bp):
TAATAATAATATAATATAAAATAAAATAAAAA
Found at i:3729113 original size:3 final size:3
Alignment explanation
Indices: 3729013--3729094 Score: 82
Period size: 3 Copynumber: 27.7 Consensus size: 3
3729003 TTTGTGTCTG
*
3729013 TAA TAA TAA CTTAA TTAA TAA TAA TAA TAA AAA TAA TAA TAA T-A TAA
1 TAA TAA TAA --TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3729060 TAG TAA -AA TAA -AA TAA TAT TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3729095 TTATTATTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
2 8 0.12
3 52 0.78
4 4 0.06
5 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3731924 original size:11 final size:11
Alignment explanation
Indices: 3731908--3731945 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3731898 CTCGAGCTCA
3731908 ATTCAAACTTG
1 ATTCAAACTTG
*
3731919 ATTCAAACTTA
1 ATTCAAACTTG
*
3731930 ATTCAAACTCG
1 ATTCAAACTTG
3731941 ATTCA
1 ATTCA
3731946 TTACCACGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (11 bp):
ATTCAAACTTG
Found at i:3735701 original size:14 final size:14
Alignment explanation
Indices: 3735662--3735752 Score: 56
Period size: 14 Copynumber: 6.5 Consensus size: 14
3735652 ATATAATTGA
*
3735662 GTTTAGAGTTTAGG
1 GTTTAGGGTTTAGG
* * *
3735676 GTTTAAGATTTAAG
1 GTTTAGGGTTTAGG
*
3735690 GTTTAGGGTTTATG
1 GTTTAGGGTTTAGG
* * * * *
3735704 GTTCATGATTCAAG
1 GTTTAGGGTTTAGG
* *
3735718 ATTAAGGGTTTAGG
1 GTTTAGGGTTTAGG
**
3735732 GTTTAGATTTTAGG
1 GTTTAGGGTTTAGG
3735746 GTTTAGG
1 GTTTAGG
3735753 CCTTAGGATT
Statistics
Matches: 54, Mismatches: 23, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
14 54 1.00
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (14 bp):
GTTTAGGGTTTAGG
Found at i:3735706 original size:28 final size:28
Alignment explanation
Indices: 3735662--3735752 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
3735652 ATATAATTGA
*
3735662 GTTTAGAGTTTAGGGTTTAAGATTTAAG
1 GTTTAGGGTTTAGGGTTTAAGATTTAAG
* * * *
3735690 GTTTAGGGTTTATGGTTCATGATTCAAG
1 GTTTAGGGTTTAGGGTTTAAGATTTAAG
* * *
3735718 ATTAAGGGTTTAGGGTTT-AGATTTTAGG
1 GTTTAGGGTTTAGGGTTTAAGA-TTTAAG
3735746 GTTTAGG
1 GTTTAGG
3735753 CCTTAGGATT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
27 2 0.04
28 46 0.96
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (28 bp):
GTTTAGGGTTTAGGGTTTAAGATTTAAG
Found at i:3735873 original size:11 final size:11
Alignment explanation
Indices: 3735857--3735919 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3735847 GTATTATAGA
3735857 ATTTTTAATAT
1 ATTTTTAATAT
3735868 ATTTTTAA-A-
1 ATTTTTAATAT
3735877 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
3735888 ATCAATAATGT
1 ATTTTTAATAT
3735899 ATTTTTAATAT
1 ATTTTTAATAT
*
3735910 ATTCTTAATA
1 ATTTTTAATA
3735920 ATGTAATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 27 0.68
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:3736987 original size:2 final size:2
Alignment explanation
Indices: 3736975--3737004 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3736965 CTAATCATCA
*
3736975 AT AT CT 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
3737005 GTTTACTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3738715 original size:24 final size:24
Alignment explanation
Indices: 3738660--3738762 Score: 136
Period size: 24 Copynumber: 4.3 Consensus size: 24
3738650 AAACGAATGT
* *
3738660 TAAACGAACATGTTCGTGAATGC-
1 TAAACGAACACGTTCGTGAATACA
* * *
3738683 TAAATGAACACATTCGTGAATGCA
1 TAAACGAACACGTTCGTGAATACA
*
3738707 TAAACGAACACGTTTGTGAATACA
1 TAAACGAACACGTTCGTGAATACA
*
3738731 TAAACGAACACGTTTGTGAATACA
1 TAAACGAACACGTTCGTGAATACA
3738755 TAAACGAA
1 TAAACGAA
3738763 TACATTCACG
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
23 20 0.28
24 52 0.72
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
TAAACGAACACGTTCGTGAATACA
Found at i:3747421 original size:44 final size:45
Alignment explanation
Indices: 3747328--3747426 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
3747318 ACATGAAGTG
* ** *
3747328 CATCGATGCACTCTTTTAAAATACAAACATCGAATGCCATTAATG
1 CATCGATGCACCCCCTTAAAATACAAACATCGAATGCCATTAATA
* * *
3747373 CATCGATGCACCCCCTT-AAATATAAACATCGAATAG-GATTTATA
1 CATCGATGCACCCCCTTAAAATACAAACATCGAAT-GCCATTAATA
3747417 CATCGATGCA
1 CATCGATGCA
3747427 TGGTGTGTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
44 31 0.67
45 15 0.33
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (45 bp):
CATCGATGCACCCCCTTAAAATACAAACATCGAATGCCATTAATA
Found at i:3748130 original size:23 final size:23
Alignment explanation
Indices: 3748081--3748138 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
3748071 TGGCACTACG
* * *
3748081 GTGCAATTCTACGCGACACTTCG
1 GTGCAATTATACGCGACAATTCA
* *
3748104 GTGCAATTATACGTGGCAATTCA
1 GTGCAATTATACGCGACAATTCA
*
3748127 GTGCATTTATAC
1 GTGCAATTATAC
3748139 AAGCTGTGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (23 bp):
GTGCAATTATACGCGACAATTCA
Found at i:3753706 original size:10 final size:10
Alignment explanation
Indices: 3753691--3753715 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3753681 GTTTCCAGAT
3753691 TTCTTTCTTC
1 TTCTTTCTTC
3753701 TTCTTTCTTC
1 TTCTTTCTTC
3753711 TTCTT
1 TTCTT
3753716 CAACGTGAAG
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:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:3754747 original size:31 final size:30
Alignment explanation
Indices: 3754698--3754757 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3754688 TTATATAAGC
*
3754698 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
3754729 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
3754758 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:3754989 original size:23 final size:23
Alignment explanation
Indices: 3754963--3755017 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
3754953 TCTTATCTGT
* *
3754963 CACTACGGTACAATTCTATGCGG
1 CACTTCGGTACAATTCTACGCGG
** *
3754986 CACTTCGGTGTAATTCTACGTGG
1 CACTTCGGTACAATTCTACGCGG
3755009 CACTTCGGT
1 CACTTCGGT
3755018 GAATTTATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
CACTTCGGTACAATTCTACGCGG
Found at i:3755018 original size:23 final size:22
Alignment explanation
Indices: 3754974--3755022 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
3754964 ACTACGGTAC
*
3754974 AATTCTATGCGGCACTTCGGTG
1 AATTCTACGCGGCACTTCGGTG
*
3754996 TAATTCTACGTGGCACTTCGGTG
1 -AATTCTACGCGGCACTTCGGTG
3755019 AATT
1 AATT
3755023 TATACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (22 bp):
AATTCTACGCGGCACTTCGGTG
Found at i:3755028 original size:23 final size:23
Alignment explanation
Indices: 3754984--3755028 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3754974 AATTCTATGC
*
3754984 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGTAATTATACGT
3755007 GGCACTTCGGTG-AATTTATACG
1 GGCACTTCGGTGTAA-TTATACG
3755029 AGCTGTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGTAATTATACGT
Found at i:3764514 original size:24 final size:24
Alignment explanation
Indices: 3764487--3764532 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3764477 CCGTGAACTT
* *
3764487 CCCATATCCATGCATGAATTGCAC
1 CCCAAATCCATGAATGAATTGCAC
*
3764511 CCCAAATCTATGAATGAATTGC
1 CCCAAATCCATGAATGAATTGC
3764533 CGTAAATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (24 bp):
CCCAAATCCATGAATGAATTGCAC
Found at i:3764963 original size:16 final size:16
Alignment explanation
Indices: 3764944--3764982 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3764934 ACCCGATTTG
3764944 ACCTAAATAAAAAGTA
1 ACCTAAATAAAAAGTA
** *
3764960 ACCTAAATTGAAATTA
1 ACCTAAATAAAAAGTA
3764976 ACCTAAA
1 ACCTAAA
3764983 ACGAAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.23
Consensus pattern (16 bp):
ACCTAAATAAAAAGTA
Found at i:3765465 original size:18 final size:19
Alignment explanation
Indices: 3765442--3765478 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3765432 TGTTTACTTG
*
3765442 AAAATTT-TAATTGAAAAT
1 AAAATTTATAATTAAAAAT
3765460 AAAATTTATAATTAAAAAT
1 AAAATTTATAATTAAAAAT
3765479 TTTATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAATTTATAATTAAAAAT
Found at i:3765776 original size:32 final size:32
Alignment explanation
Indices: 3765706--3765781 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
3765696 TGACCTGAAG
* * *
3765706 TGAAAATTGATCGATCAGATATTTACTTGACC
1 TGAAAATCGATCAATCAGATATTAACTTGACC
** * * *
3765738 CAAAAATGGATCAATCATATATTAATTTGACC
1 TGAAAATCGATCAATCAGATATTAACTTGACC
3765770 TGAAAATCGATC
1 TGAAAATCGATC
3765782 TATCTGGTAT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (32 bp):
TGAAAATCGATCAATCAGATATTAACTTGACC
Found at i:3767788 original size:5 final size:5
Alignment explanation
Indices: 3767779--3768097 Score: 142
Period size: 5 Copynumber: 63.8 Consensus size: 5
3767769 TAAAATAAAA
* *
3767779 ATAAT GTAAT AT-A- ATAAT ATAAAT AATAAT ATAAT ATAAT -TTA- ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT -ATAAT ATAAT ATAAT ATAAT ATAAT
*
3767827 ATAAAT AATAAT ATAAT ATAAT AT-AT ACT-AT ATAAA AT-AT ATAAT
1 AT-AAT -ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT
* * **
3767872 ATAAT ATAAT ACT-AT ATAAT ATACT ATGAT AT-AT AATAA- ATGCT ATAAT
1 ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT
* *
3767921 AT-AT TTACT ATAAT ATATAT AATAAT ATAAT A-ATAT ACTAA- A-AAT
1 ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT ATA-AT A-TAAT ATAAT
* * * *
3767966 ACTAAT AT-AT ATAAT ATAAT ACT-AT ATAAT AGAAC ATACT ATAAC ATAAT
1 A-TAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT
**
3768016 ACTAA- AT-AT ATAAT AT-AT ACTATAT ATTAAT A-AAT AT-AT ACCAT
1 A-TAAT ATAAT ATAAT ATAAT A-TA-AT A-TAAT ATAAT ATAAT ATAAT
*
3768060 AT-AT ATATAT GTAAT ATAACACT ATAAT ATAAAT ATAA
1 ATAAT ATA-AT ATAAT AT-A-A-T ATAAT AT-AAT ATAA
3768098 AAGGTGTCAA
Statistics
Matches: 242, Mismatches: 30, Indels: 84
0.68 0.08 0.24
Matches are distributed among these distances:
3 5 0.02
4 45 0.19
5 133 0.55
6 41 0.17
7 15 0.06
8 3 0.01
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:3767812 original size:17 final size:17
Alignment explanation
Indices: 3767792--3768094 Score: 118
Period size: 17 Copynumber: 17.7 Consensus size: 17
3767782 ATGTAATATA
3767792 ATAATATAAATAATAAT
1 ATAATATAAATAATAAT
*
3767809 ATAATAT-AAT--TTA-
1 ATAATATAAATAATAAT
3767822 ATAATATAAATAATAAT
1 ATAATATAAATAATAAT
*
3767839 ATAATAT-AATATATACT
1 ATAATATAAATA-ATAAT
3767856 AT-ATA-AAATATATAAT
1 ATAATATAAATA-ATAAT
*
3767872 ATAATAT-AATACT-AT
1 ATAATATAAATAATAAT
* *
3767887 ATAATAT-ACT-ATGAT
1 ATAATATAAATAATAAT
*
3767902 AT-ATAATAAATGCTATAAT
1 ATAAT-ATAAAT--AATAAT
* *
3767921 AT-ATTTACTATAATATAT
1 ATAATATA-AATAATA-AT
*
3767939 ATAATA-ATATAATAAT
1 ATAATATAAATAATAAT
* * *
3767955 ATACTAAAAATACTAAT
1 ATAATATAAATAATAAT
3767972 AT-ATATAATATAATACTAT
1 ATAATATAA-ATAATA--AT
* *
3767991 ATAATAGAACATACTATAAC
1 ATAATATAA-ATA--ATAAT
3768011 ATAATACTAAATATATAAT
1 ATAATA-TAAATA-ATAAT
* *
3768030 AT-ATACTATATATTAAT
1 ATAATA-TAAATAATAAT
* **
3768047 A-AATATATACCATATAT
1 ATAATATAAATAATA-AT
* * *
3768064 ATATATGTAATATAACACT
1 ATA-ATATAA-ATAATAAT
3768083 ATAATATAAATA
1 ATAATATAAATA
3768095 TAAAAGGTGT
Statistics
Matches: 220, Mismatches: 36, Indels: 60
0.70 0.11 0.19
Matches are distributed among these distances:
13 7 0.03
14 8 0.04
15 17 0.08
16 43 0.20
17 66 0.30
18 22 0.10
19 31 0.14
20 21 0.10
21 2 0.01
22 3 0.01
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (17 bp):
ATAATATAAATAATAAT
Found at i:3767824 original size:30 final size:30
Alignment explanation
Indices: 3767771--3768032 Score: 182
Period size: 30 Copynumber: 8.4 Consensus size: 30
3767761 AAGACACTTA
*
3767771 AAATAA-AA-ATAATGTAATATAATAATAT
1 AAATAATAATATAATATAATATAATAATAT
*
3767799 AAATAATAATATAATATAATTTAATAATAT
1 AAATAATAATATAATATAATATAATAATAT
*
3767829 AAATAATAATATAATATAATAT-ATACTAT
1 AAATAATAATATAATATAATATAATAATAT
*
3767858 ATAA-AAT-ATATAATATAATATAATACTAT
1 A-AATAATAATATAATATAATATAATAATAT
* **
3767887 ATAAT-ATACTATGATATATAATA-AATGCTAT
1 A-AATAATAATAT-A-ATATAATATAATAATAT
* *
3767918 AATATATTTACTATAATAT-ATATAATAATAT
1 AA-ATA-ATAATATAATATAATATAATAATAT
*
3767949 -AATAATATACTAAAAATACTAATATATATAATAT
1 AAATAATA-A-T-ATAATA-TAATATA-ATAATAT
* * *
3767983 AATACTATATAATAGAACATACTATAACATAATACT
1 AA-A-TA-ATAATATAATATAATAT-A-ATAATA-T
3768019 AAATATATAATATA
1 AAATA-ATAATATA
3768033 TACTATATAT
Statistics
Matches: 193, Mismatches: 17, Indels: 42
0.77 0.07 0.17
Matches are distributed among these distances:
28 22 0.11
29 28 0.15
30 50 0.26
31 26 0.13
32 10 0.05
33 11 0.06
34 22 0.11
35 13 0.07
36 5 0.03
37 3 0.02
38 3 0.02
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATAATAATATAATATAATATAATAATAT
Found at i:3767874 original size:58 final size:58
Alignment explanation
Indices: 3767773--3768041 Score: 191
Period size: 58 Copynumber: 4.6 Consensus size: 58
3767763 GACACTTAAA
* * * *
3767773 ATAAA-AATAATGTAATATAATA-ATA-TAAATAATA-ATATAATATAATTTAATAAT
1 ATAAATAATAATATAATATAATATATACTATATAAAATATATAATATAATATAATAAT
*
3767827 ATAAATAATAATATAATATAATATATACTATATAAAATATATAATATAATATAATACT
1 ATAAATAATAATATAATATAATATATACTATATAAAATATATAATATAATATAATAAT
* * * **
3767885 ATATAAT-ATACTATGATATATAATAAATGCTATAATATATTTACTATAATAT-ATATAATAAT
1 ATA-AATAATAATAT-A-ATATAATATATACTAT-ATA-AAATA-TATAATATAATATAATAAT
* * * *
3767947 AT-AATAATATACTAAAAATACTAATATATA-TAATATAATACTATATAATAGAACATACTATAA
1 ATAAATAATA-A-T-ATAATA-TAATATATACT-ATATAA-AATATATAATATAATATA--ATAA
*
3768010 C
58 T
*
3768011 AT-AATACTAA-AT-ATATAATATATACTATATA
1 ATAAATAATAATATAATATAATATATACTATATA
3768042 TTAATAAATA
Statistics
Matches: 172, Mismatches: 22, Indels: 38
0.74 0.09 0.16
Matches are distributed among these distances:
54 5 0.03
55 16 0.09
56 3 0.02
57 7 0.04
58 41 0.24
59 8 0.05
60 18 0.10
61 14 0.08
62 27 0.16
63 20 0.12
64 13 0.08
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (58 bp):
ATAAATAATAATATAATATAATATATACTATATAAAATATATAATATAATATAATAAT
Found at i:3768027 original size:104 final size:102
Alignment explanation
Indices: 3767822--3768053 Score: 234
Period size: 104 Copynumber: 2.3 Consensus size: 102
3767812 ATATAATTTA
*
3767822 ATAATATA-AATA-ATAAT-ATAATATAATATATACTATATAAAATATATAATATAATATAATAC
1 ATAATATATAATATATATTAATAATATAATATATACTATATAAAATATATAATATAATATAATAC
* * *
3767884 TATATAATATACTATGATATATAATAAATGCTATAAT
66 TATATAATAAACTATGATATATAATAAATACTAAAAT
*
3767921 ATATTTACTATAATATATA-TAATAATATAATA-ATA-TACTA-AAAATACTAATATATATAATA
1 ATA-ATA-TATAATATATATTAATAATATAATATATACTA-TATAAAATA-T-ATA-ATATAATA
3767982 TAATACTATATAATAGAAC-AT-ACTATA-ACAT-AATACTAAATAT
60 TAATACTATATAATA-AACTATGA-TATATA-ATAAATACTAAA-AT
*
3768025 ATAATATATACTATATATTAATAAATATA
1 ATAATATATAATATATATTAAT-AATATA
3768054 TACCATATAT
Statistics
Matches: 112, Mismatches: 6, Indels: 25
0.78 0.04 0.17
Matches are distributed among these distances:
99 3 0.03
100 2 0.02
101 10 0.09
102 21 0.19
103 32 0.29
104 42 0.38
105 2 0.02
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (102 bp):
ATAATATATAATATATATTAATAATATAATATATACTATATAAAATATATAATATAATATAATAC
TATATAATAAACTATGATATATAATAAATACTAAAAT
Found at i:3768061 original size:28 final size:28
Alignment explanation
Indices: 3768018--3768075 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3768008 AACATAATAC
*
3768018 TAAATATATAATATATACTATATAT-TAA
1 TAAATATATAACATATA-TATATATGTAA
*
3768046 TAAATATATACCATATATATATATGTAA
1 TAAATATATAACATATATATATATGTAA
3768074 TA
1 TA
3768076 TAACACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAATATATAACATATATATATATGTAA
Found at i:3768089 original size:28 final size:27
Alignment explanation
Indices: 3768018--3768096 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
3768008 AACATAATAC
* *
3768018 TAAATATATAATATATACTATATATTAA
1 TAAACATATAATATATA-TATATAGTAA
*
3768046 TAAATATATACCATATATATATAT-GTAA
1 TAAACATATA--ATATATATATATAGTAA
*
3768074 TATAACACTATAATATAAATATA
1 TA-AACA-TATAATATATATATA
3768097 AAAGGTGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 25 0.57
29 8 0.18
30 11 0.25
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.39
Consensus pattern (27 bp):
TAAACATATAATATATATATATAGTAA
Found at i:3781076 original size:5 final size:5
Alignment explanation
Indices: 3781054--3781327 Score: 122
Period size: 5 Copynumber: 54.2 Consensus size: 5
3781044 TAACAATTAT
* * * *
3781054 TAATA AAATA -AAAA TAATG TAATA TAATA -ACTA TAATA TGTAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA --TAATA TAATA
* *
3781104 TAATAA TAATA TAATA T-ATA CT-ATA TATTA T-ATA TTATA TAATA CTATATA
1 TAAT-A TAATA TAATA TAATA -TAATA TAATA TAATA TAATA TAATA -TA-ATA
* * * * * * **
3781155 AAATA TAATA TGATA CT-ACA TAATA TACTA TGATA T-ATA -AAAA TGCTA
1 TAATA TAATA TAATA -TAATA TAATA TAATA TAATA TAATA TAATA TAATA
* *
3781203 TAATA TAATA -AATA TAATA -GATA TAATAA TATATA TATATA TAACA
1 TAATA TAATA TAATA TAATA TAATA TAAT-A TA-ATA TA-ATA TAATA
* * * * *
3781249 TACTA TATATA GAACA TACTA TAATA TAATA CTAAATA TACTA T-ATA
1 TAATA TA-ATA TAATA TAATA TAATA TAATA -T-AATA TAATA TAATA
* *
3781296 TTATA TATATA TAATA -ATATA TACTA TAATA T
1 TAATA TA-ATA TAATA TA-ATA TAATA TAATA T
3781328 GTAATACACT
Statistics
Matches: 203, Mismatches: 41, Indels: 50
0.69 0.14 0.17
Matches are distributed among these distances:
4 30 0.15
5 127 0.63
6 32 0.16
7 14 0.07
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:3781130 original size:2 final size:2
Alignment explanation
Indices: 3781096--3781327 Score: 89
Period size: 2 Copynumber: 122.0 Consensus size: 2
3781086 ATAATATGTA
3781096 AT AT A- AT AT A- AT A- AT A- AT AT A- AT AT AT ACT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
3781133 AT AT AT -T AT AT A- AT ACT AT AT A- AA AT AT A- AT AT GAT ACT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT -AT A-T
* * * *
3781172 AC AT A- AT AT ACT AT GAT AT AT AA AA AT GCT AT A- AT AT A- AT
1 AT AT AT AT AT A-T AT -AT AT AT AT AT AT -AT AT AT AT AT AT AT
* * *
3781212 AA AT AT A- AT AG AT AT A- AT A- AT AT AT AT AT AT AT A- AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3781250 ACT AT AT AT AG A- AC AT ACT AT A- AT AT A- AT ACT AA AT AT ACT
1 A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T
3781291 AT AT AT -T AT AT AT AT AT A- AT A- AT AT AT ACT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
3781328 GTAATACACT
Statistics
Matches: 178, Mismatches: 16, Indels: 72
0.67 0.06 0.27
Matches are distributed among these distances:
1 24 0.13
2 131 0.74
3 23 0.13
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (2 bp):
AT
Found at i:3781551 original size:13 final size:13
Alignment explanation
Indices: 3781530--3781574 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
3781520 AACGTAAACG
3781530 AACACAAACGAAC
1 AACACAAACGAAC
*
3781543 AACATAAACG---
1 AACACAAACGAAC
*
3781553 AACATAAACGAAC
1 AACACAAACGAAC
3781566 AACACAAAC
1 AACACAAAC
3781575 ACAAAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 10 0.37
13 17 0.63
ACGTcount: A:0.62, C:0.27, G:0.07, T:0.04
Consensus pattern (13 bp):
AACACAAACGAAC
Found at i:3781551 original size:23 final size:23
Alignment explanation
Indices: 3781524--3781574 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3781514 TAAACAAACG
3781524 TAAACGAACACAAACGAACAACA
1 TAAACGAACACAAACGAACAACA
*
3781547 TAAACGAACATAAACGAACAACA
1 TAAACGAACACAAACGAACAACA
*
3781570 CAAAC
1 TAAAC
3781575 ACAAAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.61, C:0.25, G:0.08, T:0.06
Consensus pattern (23 bp):
TAAACGAACACAAACGAACAACA
Found at i:3784075 original size:18 final size:20
Alignment explanation
Indices: 3784044--3784085 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
3784034 TGGAAAAGAT
3784044 GAGAGAGAACGGTC-AG-GA
1 GAGAGAGAACGGTCGAGTGA
**
3784062 GAGAGAGAGTGGTCGAGTGA
1 GAGAGAGAACGGTCGAGTGA
3784082 GAGA
1 GAGA
3784086 AAAAACAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 2 0.10
20 6 0.30
ACGTcount: A:0.36, C:0.07, G:0.48, T:0.10
Consensus pattern (20 bp):
GAGAGAGAACGGTCGAGTGA
Found at i:3788403 original size:40 final size:40
Alignment explanation
Indices: 3788348--3788429 Score: 148
Period size: 40 Copynumber: 2.0 Consensus size: 40
3788338 TGCAGGTTTA
3788348 TAATACATTACGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACATTACGGTGTATATGGTGGGCACGACCTTATGTG
3788388 TAATACACTT-CGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACA-TTACGGTGTATATGGTGGGCACGACCTTATGTG
3788428 TA
1 TA
3788430 GCACTACGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 39 0.95
41 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACATTACGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:3788883 original size:11 final size:11
Alignment explanation
Indices: 3788867--3788892 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3788857 AATTAGTGGC
3788867 ATGTAATTATT
1 ATGTAATTATT
3788878 ATGTAATTATT
1 ATGTAATTATT
3788889 ATGT
1 ATGT
3788893 TTTATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (11 bp):
ATGTAATTATT
Found at i:3791494 original size:11 final size:11
Alignment explanation
Indices: 3791474--3791503 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3791464 ACAGGAGGTT
3791474 GAGAACTAGGC
1 GAGAACTAGGC
*
3791485 GAGAATTAGGC
1 GAGAACTAGGC
3791496 GAGAACTA
1 GAGAACTA
3791504 TTGGTTGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (11 bp):
GAGAACTAGGC
Found at i:3797532 original size:30 final size:30
Alignment explanation
Indices: 3797498--3797580 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
3797488 CATATTCGAT
3797498 TTAAAGGACCAAAATAGCAAAAATAGAAAC
1 TTAAAGGACCAAAATAGCAAAAATAGAAAC
* * *
3797528 TTAAAGGACTAAAATATCAAAAATAGAAAT
1 TTAAAGGACCAAAATAGCAAAAATAGAAAC
*
3797558 TTAAAGGACCATAATAGCAAAAA
1 TTAAAGGACCAAAATAGCAAAAA
3797581 AACTCAGAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.59, C:0.11, G:0.12, T:0.18
Consensus pattern (30 bp):
TTAAAGGACCAAAATAGCAAAAATAGAAAC
Found at i:3798921 original size:3 final size:3
Alignment explanation
Indices: 3798913--3798967 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
3798903 AAATGTAAAT
3798913 ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
*
3798959 ATT ATA ATA
1 ATA ATA ATA
3798968 TTTTTTAGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3799525 original size:36 final size:37
Alignment explanation
Indices: 3799477--3799610 Score: 155
Period size: 36 Copynumber: 3.6 Consensus size: 37
3799467 TTTCTCAAAG
* * *
3799477 GAAAAATGTCTCAAGCGAGACGAATTTTGTTTTGAGA
1 GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAGA
* * * *
3799514 G-AAATTGTCTCAAACGAGACCAAATTTATTTTTAGC
1 GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAGA
* *
3799550 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTTA-A
1 GAAAATTGTCTCAAGCGAGACGAAATTTG-TTTTTAGA
3799587 GAAAACTTGTCTCAAGCGAGACGA
1 GAAAA-TTGTCTCAAGCGAGACGA
3799611 CCCTTTGTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
36 29 0.36
37 29 0.36
38 22 0.28
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (37 bp):
GAAAATTGTCTCAAGCGAGACGAAATTTGTTTTTAGA
Found at i:3799560 original size:37 final size:37
Alignment explanation
Indices: 3799477--3799608 Score: 142
Period size: 37 Copynumber: 3.6 Consensus size: 37
3799467 TTTCTCAAAG
* * * * *
3799477 GAAAAATGTCTCAAGCGAGACGAATTTTGTTTTGAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
* * * *
3799514 G-AAATTGTCTCAAACGAGACCAAATTTATTTTTAGC
1 GAAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
*
3799550 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTTA-A
1 GAAAACTGTCTCAAGCGAGACAAAATTT-ATTTTTAGA
3799587 GAAAACTTGTCTCAAGCGAGAC
1 GAAAAC-TGTCTCAAGCGAGAC
3799609 GACCCTTTGT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
36 29 0.36
37 30 0.38
38 21 0.26
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (37 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
Found at i:3805972 original size:32 final size:32
Alignment explanation
Indices: 3805922--3805996 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
3805912 TGGTCGTACA
* * *
3805922 AGCCTACTCAAGGGAGTACATTAGGGCCTAAG
1 AGCCTACCCAAAGAAGTACATTAGGGCCTAAG
* * *
3805954 AGCCTACCCAAAGAAGTACCTTGGGGCCTTAG
1 AGCCTACCCAAAGAAGTACATTAGGGCCTAAG
3805986 AGCCTACCCAA
1 AGCCTACCCAA
3805997 GGCAACCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (32 bp):
AGCCTACCCAAAGAAGTACATTAGGGCCTAAG
Found at i:3807656 original size:20 final size:21
Alignment explanation
Indices: 3807631--3807676 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3807621 TTTGTGGTCG
3807631 TTTCTAGCCG-CTGGGGATGA
1 TTTCTAGCCGTCTGGGGATGA
* * *
3807651 TTTCTAGTCGTTTGGGGATGC
1 TTTCTAGCCGTCTGGGGATGA
3807672 TTTCT
1 TTTCT
3807677 CTGCAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.11, C:0.17, G:0.30, T:0.41
Consensus pattern (21 bp):
TTTCTAGCCGTCTGGGGATGA
Found at i:3811436 original size:30 final size:29
Alignment explanation
Indices: 3811391--3811467 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
3811381 TTACAAATAT
*
3811391 TTTTTTCTAACATTTGTAACTAAGGGCCCAA
1 TTTTTTC-AATATTTGTAAC-AAGGGCCCAA
* * ** *
3811422 TTTTTTCAATATTTGATATCAATGGCTTAT
1 TTTTTTCAATATTTG-TAACAAGGGCCCAA
3811452 TTTTTTCAATATTTGT
1 TTTTTTCAATATTTGT
3811468 TATTAGGTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 28 0.72
31 10 0.26
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (29 bp):
TTTTTTCAATATTTGTAACAAGGGCCCAA
Found at i:3812388 original size:2 final size:2
Alignment explanation
Indices: 3812381--3812434 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3812371 GATTATACCA
3812381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3812423 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3812435 TTAAAAAAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3814301 original size:20 final size:20
Alignment explanation
Indices: 3814278--3814323 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3814268 TAAAATTTCA
3814278 AAATTGTATTTAAATAGTCC
1 AAATTGTATTTAAATAGTCC
*
3814298 AAATTTTATTTAAATAGTCC
1 AAATTGTATTTAAATAGTCC
3814318 AAATTG
1 AAATTG
3814324 CCTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
AAATTGTATTTAAATAGTCC
Found at i:3814329 original size:20 final size:20
Alignment explanation
Indices: 3814278--3814329 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3814268 TAAAATTTCA
*
3814278 AAATTGTATTTAAATAGTCC
1 AAATTGCATTTAAATAGTCC
**
3814298 AAATTTTATTTAAATAGTCC
1 AAATTGCATTTAAATAGTCC
*
3814318 AAATTGCCTTTA
1 AAATTGCATTTA
3814330 TTTTCCCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (20 bp):
AAATTGCATTTAAATAGTCC
Found at i:3828795 original size:25 final size:25
Alignment explanation
Indices: 3828766--3828840 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
3828756 GCTAAACAAG
* *
3828766 TCATAGTCTAGTAAATCTCATAAAA
1 TCATACTCTAATAAATCTCATAAAA
3828791 TCATACTAC-AATAAATCTCATAAAA
1 TCATACT-CTAATAAATCTCATAAAA
* *
3828816 TCATATTATAATAAATCTCATAAAA
1 TCATACTCTAATAAATCTCATAAAA
3828841 GAGTTAACCT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 43 0.98
26 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (25 bp):
TCATACTCTAATAAATCTCATAAAA
Found at i:3835915 original size:25 final size:25
Alignment explanation
Indices: 3835886--3835935 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3835876 ACTAAACAAG
* *
3835886 TCATAGTCCAGTAAACCTCATAAAA
1 TCATACTCCAATAAACCTCATAAAA
* *
3835911 TCATACTGCAATAAATCTCATAAAA
1 TCATACTCCAATAAACCTCATAAAA
3835936 GAGTTAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
TCATACTCCAATAAACCTCATAAAA
Found at i:3836002 original size:31 final size:31
Alignment explanation
Indices: 3835967--3836075 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
3835957 TTAGGGCCTG
*
3835967 AGAGCCTACCCAAGAAATATTTCGGGGCCAC
1 AGAGCCTACCCAAGAAATATTTCAGGGCCAC
* * *
3835998 AGAGCCTACCTAAGAACACATCTT-AGGACCAC
1 AGAGCCTACCCAAGAA-ATAT-TTCAGGGCCAC
* * * *
3836030 AGGGCCTACCCGAG-AATGATCTCAGGGCCGC
1 AGAGCCTACCCAAGAAAT-ATTTCAGGGCCAC
*
3836061 AGAGCCTACCTAAGA
1 AGAGCCTACCCAAGA
3836076 GTCACATTAG
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
30 2 0.03
31 35 0.59
32 20 0.34
33 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAATATTTCAGGGCCAC
Found at i:3843696 original size:38 final size:39
Alignment explanation
Indices: 3843640--3843717 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
3843630 GTTTTAAGTT
*
3843640 GAGAACACCTAATATATTC-TTGGCATGTTTACCCTATA
1 GAGAACACCAAATATATTCTTTGGCATGTTTACCCTATA
* *
3843678 GAGAACACCAAATGTATTCTTTGGGATGTTTACCCTATA
1 GAGAACACCAAATATATTCTTTGGCATGTTTACCCTATA
3843717 G
1 G
3843718 GTCGTATACG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 17 0.47
39 19 0.53
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (39 bp):
GAGAACACCAAATATATTCTTTGGCATGTTTACCCTATA
Found at i:3844775 original size:49 final size:48
Alignment explanation
Indices: 3844717--3844817 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 48
3844707 CATTTCTCTT
* * * *
3844717 TTATTTTTTTAATATTTAATTTATCGATC-TATTAATCTAAATCAAATA
1 TTATTTTTTTAACATTTAACTTATCAATCGT-TTAATCTAAATAAAATA
*
3844765 CTTATTTTTTTAACATTTAACTTATTAATCGTTTAATCTAAATAAAATA
1 -TTATTTTTTTAACATTTAACTTATCAATCGTTTAATCTAAATAAAATA
3844814 TTAT
1 TTAT
3844818 AGAAATTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 4 0.09
49 41 0.89
50 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (48 bp):
TTATTTTTTTAACATTTAACTTATCAATCGTTTAATCTAAATAAAATA
Found at i:3847913 original size:21 final size:20
Alignment explanation
Indices: 3847870--3847921 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3847860 TTTTCCCAAT
*
3847870 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
3847890 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
3847911 TCGCAACGCGA
1 TCGCAATGCGA
3847922 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:3847935 original size:20 final size:20
Alignment explanation
Indices: 3847911--3848003 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
3847901 ATTTGGAAAA
*
3847911 TCGCAACGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
3847931 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
3847951 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
3847971 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
3847991 TCGCAACGAGATA
1 TCGCAACGCGATA
3848004 ATACATAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:3848218 original size:22 final size:22
Alignment explanation
Indices: 3848190--3848233 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3848180 CACTCTATCA
*
3848190 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
*
3848212 CCCATCTCAGGCGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
3848234 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCAGACGAAATCCGTC
Found at i:3848516 original size:20 final size:21
Alignment explanation
Indices: 3848476--3848535 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
3848466 TTTTATTCTC
* **
3848476 TCGTTGCGATAGTCAAATTCG
1 TCGTTGCGATTGTCATTTTCG
3848497 -CGTTGCGATTGTCATTTTCG
1 TCGTTGCGATTGTCATTTTCG
*
3848517 TC-TTGCGATTTTCATTTTC
1 TCGTTGCGATTGTCATTTTC
3848536 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (21 bp):
TCGTTGCGATTGTCATTTTCG
Found at i:3848726 original size:25 final size:24
Alignment explanation
Indices: 3848672--3848726 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3848662 TGTTTATTAT
* *
3848672 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3848696 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3848722 TGTTT
1 TGTTT
3848727 ATTGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3849866 original size:20 final size:18
Alignment explanation
Indices: 3849843--3849920 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 18
3849833 CGCAACACGA
3849843 AAATGACTATCGCAATGCGG
1 AAATGA-TATCGCAATGC-G
3849863 AAATGGATATCGCAATGCG
1 AAAT-GATATCGCAATGCG
*
3849882 AAATGAAAATCGCAA--CG
1 AAATG-ATATCGCAATGCG
3849899 ACAA--A-ATCGCAATGCG
1 A-AATGATATCGCAATGCG
3849915 AAATGA
1 AAATGA
3849921 AAATCGCAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
14 7 0.14
15 3 0.06
16 3 0.06
17 4 0.08
18 3 0.06
19 13 0.26
20 15 0.30
21 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.17
Consensus pattern (18 bp):
AAATGATATCGCAATGCG
Found at i:3849886 original size:19 final size:20
Alignment explanation
Indices: 3849843--3849896 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3849833 CGCAACACGA
*
3849843 AAATGACTATCGCAATGCGG
1 AAATGAATATCGCAATGCGG
*
3849863 AAATGGATATCGCAATGC-G
1 AAATGAATATCGCAATGCGG
*
3849882 AAATGAAAATCGCAA
1 AAATGAATATCGCAA
3849897 CGACAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.19
Consensus pattern (20 bp):
AAATGAATATCGCAATGCGG
Found at i:3849906 original size:14 final size:14
Alignment explanation
Indices: 3849887--3849945 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3849877 ATGCGAAATG
3849887 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3849901 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
3849920 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3849934 AAAATCGCAACG
1 AAAATCGCAACG
3849946 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3849913 original size:33 final size:33
Alignment explanation
Indices: 3849871--3849962 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
3849861 GGAAATGGAT
3849871 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3849904 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
3849937 ATCGCAACGCGAAATGAAAATTGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3849963 TTTTCGCGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3849925 original size:19 final size:19
Alignment explanation
Indices: 3849851--3849963 Score: 93
Period size: 19 Copynumber: 6.4 Consensus size: 19
3849841 GAAAATGACT
* *
3849851 ATCGCAATGCGGAAATGGAT
1 ATCGCAATGC-GAAATGAAA
3849871 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3849890 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3849904 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3849923 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3849937 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3849956 ATTGCAAT
1 ATCGCAAT
3849964 TTTCGCGTTG
Statistics
Matches: 75, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.27
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 33 0.44
20 10 0.13
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3849979 original size:14 final size:15
Alignment explanation
Indices: 3849957--3850028 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 15
3849947 GAAATGAAAA
*
3849957 TTGCAATTTTCG-CG
1 TTGCGATTTTCGTCG
3849971 TTGCGATTTT-GTCG
1 TTGCGATTTTCGTCG
*
3849985 TTGCGATTTTCATTTCG
1 TTGCGATTTTC--GTCG
*
3850002 CATTGCAATTTT-GTCG
1 --TTGCGATTTTCGTCG
3850018 TTGCGATTTTC
1 TTGCGATTTTC
3850029 ATTTCGCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
13 1 0.02
14 30 0.65
16 3 0.07
17 3 0.07
19 9 0.20
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (15 bp):
TTGCGATTTTCGTCG
Found at i:3850012 original size:19 final size:19
Alignment explanation
Indices: 3849985--3850043 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
3849975 GATTTTGTCG
*
3849985 TTGCGATTTTCATTTCGCA
1 TTGCAATTTTCATTTCGCA
*
3850004 TTGCAA-TTT--TGTCG--
1 TTGCAATTTTCATTTCGCA
*
3850018 TTGCGATTTTCATTTCGCA
1 TTGCAATTTTCATTTCGCA
3850037 TTGCAAT
1 TTGCAAT
3850044 AGCCATTTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.13
17 4 0.13
18 3 0.10
19 11 0.37
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCAATTTTCATTTCGCA
Found at i:3850013 original size:33 final size:33
Alignment explanation
Indices: 3849964--3850043 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
3849954 AAATTGCAAT
* *
3849964 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
3849997 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
3850030 TTTCGCATTGCAAT
1 TTTCGCATTGCAAT
3850044 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
Found at i:3850065 original size:20 final size:20
Alignment explanation
Indices: 3850028--3850082 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
3850018 TTGCGATTTT
* *
3850028 CATTT-CGCATTGCAATAGC
1 CATTTCCGCGTTGCGATAGC
3850047 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
3850067 CATTTCCGCGTTGCGA
1 CATTTCCGCGTTGCGA
3850083 AAGTAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:3850535 original size:40 final size:42
Alignment explanation
Indices: 3850446--3850535 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
3850436 CCCGACTCAC
* * * *
3850446 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTTAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
* *
3850488 CTATCATCCCTTAAGAGTCCCC-CC-ACCATTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
3850528 CTGTCATC
1 CTGTCATC
3850536 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 19 0.46
41 2 0.05
42 20 0.49
ACGTcount: A:0.23, C:0.39, G:0.14, T:0.23
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
Found at i:3851972 original size:14 final size:14
Alignment explanation
Indices: 3851938--3851976 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3851928 TTGATTGTTT
3851938 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3851952 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3851966 TGTTGATTTGT
1 AATTGATTTGT
3851977 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3852140 original size:19 final size:19
Alignment explanation
Indices: 3852116--3852180 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
3852106 ACAACGAGAG
3852116 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3852135 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
3852154 AACCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
3852168 AATCGCAATGCGA
1 AATCGCAATGCGA
3852181 TTTTCATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.23
15 1 0.03
16 2 0.05
17 2 0.05
19 25 0.64
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3852224 original size:20 final size:20
Alignment explanation
Indices: 3852199--3852274 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
3852189 TCGCATTGCA
*
3852199 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
3852219 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* *
3852239 ATTTTCGTGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
3852259 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
3852275 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:3852520 original size:20 final size:20
Alignment explanation
Indices: 3852497--3852573 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
3852487 ATTGCGATTT
* *
3852497 TCAGAATCTCGTTGCAAAAG
1 TCAGAATCGCGTTGCGAAAG
*
3852517 TCAGAATCGTGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
3852537 TCAGTATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
3852557 TCAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
3852574 TTTTGTATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:3852604 original size:41 final size:41
Alignment explanation
Indices: 3852541--3852618 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
3852531 CGAAAGTCAG
*
3852541 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
* *
3852582 TATCGCGTTGCGATAGTTAGTATCGCATTGCGATTTT
1 TATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT
3852619 CCAAATTCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
Found at i:3852607 original size:20 final size:20
Alignment explanation
Indices: 3852515--3852615 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
3852505 TCGTTGCAAA
* * *
3852515 AGTCAGAATCGTGTTGCGAA
1 AGTCAGTATCGCGTTGCGAT
*
3852535 AGTCAGTATCGCGTTGCGAA
1 AGTCAGTATCGCGTTGCGAT
3852555 AGTCAGTATCGCGTTGCGATTT
1 AGTCAGTATCGCGTTGCGA--T
* *
3852577 TGT-ATTATCGCGTTGCGAT
1 AGTCAGTATCGCGTTGCGAT
* *
3852596 AGTTAGTATCGCATTGCGAT
1 AGTCAGTATCGCGTTGCGAT
3852616 TTTCCAAATT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.04
20 51 0.73
21 14 0.20
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (20 bp):
AGTCAGTATCGCGTTGCGAT
Found at i:3852634 original size:41 final size:41
Alignment explanation
Indices: 3852541--3852636 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
3852531 CGAAAGTCAG
* * ** *
3852541 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAA
*
3852582 TATCGCGTTGCGATAGTTAGTATCGCATTGCGATTTTCCAAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAA
*
3852624 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
3852637 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAA
Found at i:3852648 original size:20 final size:21
Alignment explanation
Indices: 3852604--3852655 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3852594 ATAGTTAGTA
*
3852604 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
3852625 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
3852645 TCGCATTGCGA
1 TCGCATTGCGA
3852656 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3853145 original size:132 final size:132
Alignment explanation
Indices: 3852902--3853167 Score: 514
Period size: 132 Copynumber: 2.0 Consensus size: 132
3852892 TTAGGTTTTG
3852902 AATTAATTATTGGTATTCGATCTATTGACTGATTAATCTAGATCGGATTTTGCAGAAACCATTCT
1 AATTAATTATTGGTATTCGATCTATTGACTGATTAATCTAGATCGGATTTTGCAGAAACCATTCT
3852967 AGGGTGATCTCCCAACTCAGTTTGCTCTATTTACAAATGCCATGATTCAAACCTCTGACTTTACT
66 AGGGTGATCTCCCAACTCAGTTTGCTCTATTTACAAATGCCATGATTCAAACCTCTGACTTTACT
3853032 TA
131 TA
3853034 AATTAATTATTGGTATTCGATCTATTGACTGATTAATCTAGATCGGATTTTGCAGAAACCATTCT
1 AATTAATTATTGGTATTCGATCTATTGACTGATTAATCTAGATCGGATTTTGCAGAAACCATTCT
* *
3853099 AGGGTGATCTCCCAACTCAGTTTGCTCTATTTACAAATGTCGTGATTCAAACCTCTGACTTTACT
66 AGGGTGATCTCCCAACTCAGTTTGCTCTATTTACAAATGCCATGATTCAAACCTCTGACTTTACT
3853164 TA
131 TA
3853166 AA
1 AA
3853168 GAAGAGGTTT
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 132 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (132 bp):
AATTAATTATTGGTATTCGATCTATTGACTGATTAATCTAGATCGGATTTTGCAGAAACCATTCT
AGGGTGATCTCCCAACTCAGTTTGCTCTATTTACAAATGCCATGATTCAAACCTCTGACTTTACT
TA
Found at i:3854318 original size:3 final size:3
Alignment explanation
Indices: 3854310--3854389 Score: 137
Period size: 3 Copynumber: 27.0 Consensus size: 3
3854300 GTGTTAGCTG
3854310 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3854357 T-A TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
3854390 AAGTTTAGTC
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
2 4 0.05
3 67 0.91
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3859013 original size:84 final size:83
Alignment explanation
Indices: 3858831--3859000 Score: 279
Period size: 84 Copynumber: 2.0 Consensus size: 83
3858821 AAACTCATGT
*
3858831 TTTAGGATATTATTTT-ATATATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTT
1 TTTAGGATATTATTTTAATATATTATATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTT
* *
3858895 TAAGTGTTTTAATTAGGA
66 TAAGTATTTTAATTAAGA
* *
3858913 TTTAGGATATTATTTTAAATATATTTTATCTTATCTTTGTTTTATGTATTTTAGTTTAAATAGTT
1 TTTAGGATATTATTTT-AATATATTATATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTT
3858978 TTAAGTATTTTAATTAAGA
65 TTAAGTATTTTAATTAAGA
3858997 TTTA
1 TTTA
3859001 TTTCTTTATT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 16 0.20
84 65 0.80
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (83 bp):
TTTAGGATATTATTTTAATATATTATATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTT
TAAGTATTTTAATTAAGA
Found at i:3860449 original size:23 final size:23
Alignment explanation
Indices: 3860423--3860482 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
3860413 TTTTCTTAGT
3860423 GACGGGACTTCATTCCAGTTAAA
1 GACGGGACTTCATTCCAGTTAAA
3860446 GACGGGACTTCATTCCAGTTAAA
1 GACGGGACTTCATTCCAGTTAAA
3860469 GACGGGACTT-ATTC
1 GACGGGACTTCATTC
3860483 ATCTTCTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (23 bp):
GACGGGACTTCATTCCAGTTAAA
Found at i:3868083 original size:19 final size:17
Alignment explanation
Indices: 3868043--3868086 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
3868033 AAACTTGAAG
3868043 CCTCTCTTTTTATTTTT
1 CCTCTCTTTTTATTTTT
3868060 CCTCTCTTTTTATTTTT
1 CCTCTCTTTTTATTTTT
3868077 CCTCTCTTTT
1 CCTCTCTTTT
3868087 CACACCCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (17 bp):
CCTCTCTTTTTATTTTT
Found at i:3868211 original size:41 final size:42
Alignment explanation
Indices: 3868132--3868212 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 42
3868122 CTTTTTCCAT
* **
3868132 GAAGAAAAAAATTGTTCATTGTTTGGAACAGTAGAAAAAAAA
1 GAAGAAAAAAATTGTTCATTGTTTCGAACAACAGAAAAAAAA
* *
3868174 GAAGAAAAAAATTG-TCATTGTTTCGAGCAACATAAAAAA
1 GAAGAAAAAAATTGTTCATTGTTTCGAACAACAGAAAAAA
3868213 TGTTCACTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 20 0.59
42 14 0.41
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.23
Consensus pattern (42 bp):
GAAGAAAAAAATTGTTCATTGTTTCGAACAACAGAAAAAAAA
Found at i:3868266 original size:69 final size:69
Alignment explanation
Indices: 3868137--3868266 Score: 158
Period size: 69 Copynumber: 1.9 Consensus size: 69
3868127 TCCATGAAGA
* * *
3868137 AAAAAATTGTTCATTGTTTGGAACAGTAGAAAAAAAAGAAGAAAAAAATTGTCATTGTTTCGAGC
1 AAAAAATTGTTCACTGTTTGGAACAGAAGAAAAAAAAGAAGAAAAAAATTG-CATCGTTTCGAGC
3868202 AACAT
65 AACAT
* *
3868207 AAAAAA-TGTTCACTGTTTTGAACA-AAGAAAGAAAAAAGAAGAAGGAAAATTG-ATCGTTTC
1 AAAAAATTGTTCACTGTTTGGAACAGAAG-AA-AAAAAAGAAGAA-AAAAATTGCATCGTTTC
3868267 AATTGCCTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
68 2 0.04
69 25 0.48
70 18 0.35
71 7 0.13
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.25
Consensus pattern (69 bp):
AAAAAATTGTTCACTGTTTGGAACAGAAGAAAAAAAAGAAGAAAAAAATTGCATCGTTTCGAGCA
ACAT
Found at i:3877985 original size:21 final size:20
Alignment explanation
Indices: 3877952--3877990 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3877942 CATCAAGATC
*
3877952 TTTGTAGATGCCATGAAATAT
1 TTTGTAGAGGCCAT-AAATAT
*
3877973 TTTGTCGAGGCCATAAAT
1 TTTGTAGAGGCCATAAAT
3877991 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTAGAGGCCATAAATAT
Found at i:3881435 original size:81 final size:80
Alignment explanation
Indices: 3881275--3881439 Score: 210
Period size: 82 Copynumber: 2.0 Consensus size: 80
3881265 AAACTCATGT
* *
3881275 TTTAAGATATTATTTTAAATATTATATTTTATCTTTGTTTTAGTTATTTAGTTTAAATAATTATA
1 TTTAAGATATTATTTTAAATATTATATCTTATCTTTGTTTTAGGTATTTAGTTTAAATAATTATA
*
3881340 AGTGTTTTAATTAGG
66 AGTGATTTAATTAGG
* * *
3881355 ATTTAGGATA-TATTTTAAATATATTTTATCTTATC-TTGTTTTAGGTATTTTAGTTTAAATAGT
1 -TTTAAGATATTATTTT-AA-ATATTATATCTTATCTTTGTTTTAGGTA-TTTAGTTTAAATAAT
*
3881418 TTTAAGT-ATTTAATTAGG
62 TATAAGTGATTTAATTAGG
3881436 TTTA
1 TTTA
3881440 TTTTTTATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
80 10 0.14
81 31 0.42
82 33 0.45
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.56
Consensus pattern (80 bp):
TTTAAGATATTATTTTAAATATTATATCTTATCTTTGTTTTAGGTATTTAGTTTAAATAATTATA
AGTGATTTAATTAGG
Found at i:3884811 original size:18 final size:18
Alignment explanation
Indices: 3884788--3884840 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 18
3884778 TATAATCGAT
3884788 TCCTTCTCGTTGAGTGAA
1 TCCTTCTCGTTGAGTGAA
*
3884806 TCC-T-TCATTGAGTGAA
1 TCCTTCTCGTTGAGTGAA
* * *
3884822 TCATTCTCGCTGCGTGAA
1 TCCTTCTCGTTGAGTGAA
3884840 T
1 T
3884841 TCTGTCATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 13 0.46
17 2 0.07
18 13 0.46
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (18 bp):
TCCTTCTCGTTGAGTGAA
Found at i:3887967 original size:58 final size:60
Alignment explanation
Indices: 3887839--3887968 Score: 151
Period size: 58 Copynumber: 2.2 Consensus size: 60
3887829 ATAAAAACGT
* *
3887839 AAAG-TACACAAATGGTCCCCCGACTATAGGATATTGTTTTATTGAGTCCCCTGACTATTA
1 AAAGTTACA-AAATGGTCCCCCAACTATAGGATATTGTTTTAGTGAGTCCCCTGACTATTA
* * * * *
3887899 AAAGTAACAAAATGGT-CCTCAACTATAGGGTGTTGTTTT-GTGAGT-CTCTCGACTATTA
1 AAAGTTACAAAATGGTCCCCCAACTATAGGATATTGTTTTAGTGAGTCCCCT-GACTATTA
3887957 AAAGTTACAAAA
1 AAAGTTACAAAA
3887969 CGTTCACCTG
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
57 3 0.05
58 24 0.40
59 19 0.32
60 11 0.18
61 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCCAACTATAGGATATTGTTTTAGTGAGTCCCCTGACTATTA
Found at i:3893544 original size:43 final size:42
Alignment explanation
Indices: 3893477--3893914 Score: 561
Period size: 43 Copynumber: 10.2 Consensus size: 42
3893467 GAGAACCAAA
* * * *
3893477 AAACGCCGCCATAGGTCAAGATCTATAGCGGCGTTTTTGAAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
* * *
3893520 TAACGCCACAAAAGGTTGATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGG-TCATATCTATAGCGGCGTTTTTGGAAC
* * * * * *
3893563 AAACGCCGCGAACGGTCGAGATCTATAACGACATTTTTGGAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
*
3893606 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
* *
3893649 AAACGCCGCAAAAGGTCATATCTATAGCAGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
* *
3893692 AAACGCCGCAAAAGGTCGAGATCTATAGCGGTGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
* *
3893735 AAACGTCGCAAAAGGACATATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
*
3893778 AAACGCCGCAAAAAGTCATATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
* *
3893821 AAATGCCGCAAAAGGTCATATCTATAGCTGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
* *
3893863 AAACGTCGAAAAAGGTCATATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
*
3893906 AAATGCCGC
1 AAACGCCGC
3893915 TAATTACCTT
Statistics
Matches: 344, Mismatches: 45, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
42 80 0.23
43 244 0.71
44 20 0.06
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
Found at i:3896717 original size:75 final size:74
Alignment explanation
Indices: 3896553--3896760 Score: 249
Period size: 75 Copynumber: 2.8 Consensus size: 74
3896543 CAAAGTCAAA
* * **
3896553 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
3896617 TTTGGCTCCGAG
63 TTTGGCTCCGAG
*
3896629 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
3896694 TTGTTCCGAG
65 TGGCTCCGAG
* * * *
3896704 AATTCCAGTATGCTCGGAGGGAACCAATACCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAG-ATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
3896761 TGTACAACGG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 21 0.18
75 63 0.54
76 31 0.27
77 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.21
Consensus pattern (74 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:3903547 original size:9 final size:8
Alignment explanation
Indices: 3903525--3903575 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
3903515 TGTTTCAACA
3903525 TTTTGGAT
1 TTTTGGAT
3903533 ATTTTGGAT
1 -TTTTGGAT
3903542 TGTTT-GAT
1 T-TTTGGAT
3903550 TTTGTGGAT
1 TTT-TGGAT
*
3903559 TGTTGGA-
1 TTTTGGAT
3903566 TTTTGGAT
1 TTTTGGAT
3903574 TT
1 TT
3903576 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:3903559 original size:17 final size:17
Alignment explanation
Indices: 3903527--3903570 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3903517 TTTCAACATT
3903527 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
3903544 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
3903561 TTGGATTTTG
1 TTGGATTTTG
3903571 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Done.