Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 21 of 121
Found at i:3801774 original size:20 final size:20
Alignment explanation
Indices: 3801749--3801787 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3801739 AAAACCTAGG
3801749 GCTTCTCTTCTCTTCTCTTA
1 GCTTCTCTTCTCTTCTCTTA
* *
3801769 GCTTCTCTTGTTTTCTCTT
1 GCTTCTCTTCTCTTCTCTT
3801788 CAGTTGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.08, T:0.59
Consensus pattern (20 bp):
GCTTCTCTTCTCTTCTCTTA
Found at i:3806194 original size:20 final size:21
Alignment explanation
Indices: 3806169--3806216 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
3806159 ATGTGAAACA
3806169 TAAATTTTTTCAATTTTT-GT
1 TAAATTTTTTCAATTTTTAGT
* * *
3806189 TAAA-TTATTCAGTTTTTATT
1 TAAATTTTTTCAATTTTTAGT
3806209 TAAATTTT
1 TAAATTTT
3806217 AAATTACATC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 11 0.50
20 9 0.41
21 2 0.09
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
TAAATTTTTTCAATTTTTAGT
Found at i:3806389 original size:37 final size:38
Alignment explanation
Indices: 3806329--3806406 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
3806319 TGTAAACTTT
3806329 TTAAAATAATGGATTTGATTG-AAATTTATTACTTTGTG
1 TTAAAATAATGGATTTGATTGAAAATTTATTA-TTTGTG
3806367 TTAAAATAATGGATTTGA-TGAAAATTTATTATTTGTG
1 TTAAAATAATGGATTTGATTGAAAATTTATTATTTGTG
3806404 TTA
1 TTA
3806407 GCTAAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
37 11 0.28
38 28 0.72
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.47
Consensus pattern (38 bp):
TTAAAATAATGGATTTGATTGAAAATTTATTATTTGTG
Found at i:3816205 original size:2 final size:2
Alignment explanation
Indices: 3816190--3816240 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
3816180 AGCCCCATTA
3816190 CT CT C- CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3816230 CT CT CT CT CT C
1 CT CT CT CT CT C
3816241 GCGCGCGCGA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:3816398 original size:2 final size:2
Alignment explanation
Indices: 3816393--3816427 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3816383 TATATACCAC
3816393 CT CT CT CT CT 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 CT CT CT CT CT C
3816428 AAACACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3818204 original size:2 final size:2
Alignment explanation
Indices: 3818197--3818256 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
3818187 ATTGCAGATG
*
3818197 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A- 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
*
3818238 AT AG AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3818257 GTAGTCTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3820730 original size:16 final size:18
Alignment explanation
Indices: 3820709--3820741 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3820699 TTTCTTTTTT
3820709 CTTTTT-TTTTT-TTATA
1 CTTTTTATTTTTATTATA
3820725 CTTTTTATTTTTATTAT
1 CTTTTTATTTTTATTAT
3820742 TAAAATAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
CTTTTTATTTTTATTATA
Found at i:3822385 original size:60 final size:60
Alignment explanation
Indices: 3822321--3822442 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
3822311 ATTCTCGAAT
* *
3822321 CCATCATCATAATCACCATATTCAATATTATCATTGTTATCGTAGTCACCAACAATGGCA
1 CCATCATCATAATCACCATATTCAACATTATCATTGTTATCGCAGTCACCAACAATGGCA
* * * * *
3822381 CCATCATCATAATCAGCATCTTCAACCTTATCGTTGTTATGGCAGTCACCAACAATGGCA
1 CCATCATCATAATCACCATATTCAACATTATCATTGTTATCGCAGTCACCAACAATGGCA
3822441 CC
1 CC
3822443 GTTAATTCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.30
Consensus pattern (60 bp):
CCATCATCATAATCACCATATTCAACATTATCATTGTTATCGCAGTCACCAACAATGGCA
Found at i:3824342 original size:7 final size:7
Alignment explanation
Indices: 3824330--3824363 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
3824320 AAGTTGAATC
3824330 AAATTTT
1 AAATTTT
3824337 AAATTTT
1 AAATTTT
3824344 AAATTTT
1 AAATTTT
3824351 AAATTTT
1 AAATTTT
3824358 AAATTT
1 AAATTT
3824364 CTTATATCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AAATTTT
Found at i:3831624 original size:22 final size:22
Alignment explanation
Indices: 3831598--3831639 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3831588 AATTTTTAAT
*
3831598 ATAAAAAAATTATAATTTAAAA
1 ATAAAAAAATTATAAATTAAAA
3831620 ATAAAAAAATTATAAATTAA
1 ATAAAAAAATTATAAATTAA
3831640 CAGATTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAAAAAATTATAAATTAAAA
Found at i:3831995 original size:13 final size:13
Alignment explanation
Indices: 3831979--3832006 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3831969 AATTATTAAA
3831979 AAAAATTAAAATT
1 AAAAATTAAAATT
3831992 AAAAATTAAAATT
1 AAAAATTAAAATT
3832005 AA
1 AA
3832007 TAGATTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:3834765 original size:2 final size:2
Alignment explanation
Indices: 3834758--3834784 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3834748 ATAACTTACA
3834758 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3834785 ATATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3840573 original size:2 final size:2
Alignment explanation
Indices: 3840566--3840590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3840556 TAGATTCTCA
3840566 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
3840591 AGAGAGAGAG
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:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:3844123 original size:127 final size:125
Alignment explanation
Indices: 3843833--3844124 Score: 277
Period size: 127 Copynumber: 2.3 Consensus size: 125
3843823 TGAAGTTTTT
* * * * *
3843833 TTTTTTTCAAAATTACTATAATACATCTATTAAATTATATATTAAATTTTAACATAATGTAAAAT
1 TTTTTTTGAAAATTACTATAATAC-TTTA-TAAATTACATATGAAAATTTAACATAATGTAAAAT
* * * * * * *
3843898 TAATTAGATATTAAATTATTAATATATCCTTACTATTGCTTTATAAAAATTTGATATGTGACA
64 TAACTAGATATTAAATTATGAATATATCCTTACTATTAC-TCATAAAAATTTGACATGTAAAA
* * * * *
3843961 TTTTTTTTAAAATGACTATAATA-TTCCTATTAATTACATATGAAAATTTAACATGATGTAAATT
1 TTTTTTTGAAAATTACTATAATACTT--TATAAATTACATATGAAAATTTAACATAATGTAAAAT
* * *
3844025 TAACTATATATTAAATTACTGAA-GTA-CCATTGCTATTAC-CATAAAATATTTGACATGTAAAA
64 TAACTAGATATTAAATTA-TGAATATATCC-TTACTATTACTCATAAAA-ATTTGACATGTAAAA
*
3844087 TTTTGTTTGAAATTTACTATAATACTTTATAAAATTAC
1 TTTT-TTTGAAAATTACTATAATACTTTAT-AAATTAC
3844125 TTATTAAATG
Statistics
Matches: 133, Mismatches: 23, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
125 6 0.05
126 22 0.17
127 77 0.58
128 28 0.21
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (125 bp):
TTTTTTTGAAAATTACTATAATACTTTATAAATTACATATGAAAATTTAACATAATGTAAAATTA
ACTAGATATTAAATTATGAATATATCCTTACTATTACTCATAAAAATTTGACATGTAAAA
Found at i:3844208 original size:12 final size:12
Alignment explanation
Indices: 3844191--3844215 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3844181 CCCCTTTGTT
3844191 TATTTAATATGA
1 TATTTAATATGA
3844203 TATTTAATATGA
1 TATTTAATATGA
3844215 T
1 T
3844216 GCTGACATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATTTAATATGA
Found at i:3844343 original size:26 final size:27
Alignment explanation
Indices: 3844304--3844354 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
3844294 TATTATAATA
3844304 TCATCCTATCATAA-TTATAAAAATGC
1 TCATCCTATCATAATTTATAAAAATGC
* * *
3844330 TCATCTTATTATAATTTATCAAAAT
1 TCATCCTATCATAATTTATAAAAAT
3844355 TATTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (27 bp):
TCATCCTATCATAATTTATAAAAATGC
Found at i:3844402 original size:58 final size:59
Alignment explanation
Indices: 3844272--3844426 Score: 156
Period size: 58 Copynumber: 2.6 Consensus size: 59
3844262 AAGAAATATT
* * *
3844272 TCTTTTCATAATTCG-TTAAAATTATTATAATATCATCCTATCATAATTATAAAAATGCTCA
1 TCTTATCATAA-TCGATCAAAATTATTATAATATC-T-CTATCATAATTACAAAAATGCTCA
* ** * *
3844333 TCTTATTATAATTTATCAAAATTATTATAATATCT-TATCATAATTACAAAAGTATTCT-T
1 TCTTATCATAATCGATCAAAATTATTATAATATCTCTATCATAATTACAAAA--ATGCTCA
*
3844392 TC-TATCATAATCGATCAAAATTACTATAATATCTC
1 TCTTATCATAATCGATCAAAATTATTATAATATCTC
3844427 ATATATCATA
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
58 43 0.55
59 2 0.03
60 6 0.08
61 27 0.35
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (59 bp):
TCTTATCATAATCGATCAAAATTATTATAATATCTCTATCATAATTACAAAAATGCTCA
Found at i:3852582 original size:22 final size:22
Alignment explanation
Indices: 3852548--3852596 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 22
3852538 AATGTACATG
3852548 AAAATCAACTAAAAGATTTTACAA
1 AAAATCAACTAAAA-ATTTT-CAA
*
3852572 AAAAT-AA-TAAAAATTTTTAA
1 AAAATCAACTAAAAATTTTCAA
3852592 AAAAT
1 AAAAT
3852597 TATCAGATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 5 0.21
23 2 0.08
24 5 0.21
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATCAACTAAAAATTTTCAA
Found at i:3874948 original size:21 final size:21
Alignment explanation
Indices: 3874916--3874988 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
3874906 AAAAATGAAA
3874916 AAAATCAT-AAAAAATAATTTT
1 AAAAT-ATAAAAAAATAATTTT
*
3874937 AAAATATAAAAAAATAAAAACTTT
1 AAAATATAAAAAAAT---AATTTT
*
3874961 -AGATATTAAAAAAATAATTTT
1 AAAATA-TAAAAAAATAATTTT
*
3874982 GAAATAT
1 AAAATAT
3874989 CTTAAATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 2 0.05
21 18 0.43
22 4 0.10
23 4 0.10
24 14 0.33
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAATATAAAAAAATAATTTT
Found at i:3875858 original size:20 final size:21
Alignment explanation
Indices: 3875833--3875873 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3875823 ATAATTATTT
* *
3875833 TATATTTAATTTTAT-TTAAA
1 TATATTAAAATTTATATTAAA
3875853 TATATTAAAATTTATATTAAA
1 TATATTAAAATTTATATTAAA
3875874 ATACTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATTAAAATTTATATTAAA
Found at i:3876781 original size:7 final size:7
Alignment explanation
Indices: 3876769--3876818 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
3876759 TTGTCCAAAA
3876769 AAAATAC
1 AAAATAC
3876776 AAAATAC
1 AAAATAC
*
3876783 GAAATAC
1 AAAATAC
3876790 -AAA-A-
1 AAAATAC
*
3876794 AACATAC
1 AAAATAC
3876801 AAAATAC
1 AAAATAC
*
3876808 GAAATAC
1 AAAATAC
3876815 AAAA
1 AAAA
3876819 GAAATATACC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
5 3 0.09
6 4 0.11
7 28 0.80
ACGTcount: A:0.70, C:0.14, G:0.04, T:0.12
Consensus pattern (7 bp):
AAAATAC
Found at i:3876789 original size:14 final size:14
Alignment explanation
Indices: 3876770--3876818 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
3876760 TGTCCAAAAA
3876770 AAATACAAAATACG
1 AAATACAAAATACG
3876784 AAATACAAAA-A--
1 AAATACAAAATACG
*
3876795 ACATACAAAATACG
1 AAATACAAAATACG
3876809 AAATACAAAA
1 AAATACAAAA
3876819 GAAATATACC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.69, C:0.14, G:0.04, T:0.12
Consensus pattern (14 bp):
AAATACAAAATACG
Found at i:3876792 original size:25 final size:25
Alignment explanation
Indices: 3876764--3876824 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
3876754 CAAATTTGTC
3876764 CAAAAAAAATACAAAATACGAAATA
1 CAAAAAAAATACAAAATACGAAATA
*
3876789 CAAAAAACATACAAAATACGAAATA
1 CAAAAAAAATACAAAATACGAAATA
*
3876814 CAAAAGAAATA
1 CAAAAAAAATA
3876825 TACCAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.70, C:0.13, G:0.05, T:0.11
Consensus pattern (25 bp):
CAAAAAAAATACAAAATACGAAATA
Found at i:3876839 original size:32 final size:32
Alignment explanation
Indices: 3876803--3876886 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
3876793 AAACATACAA
* *
3876803 AATACGAAATACAAAAGAAATATAC-CAAAAAT
1 AATACAAAATACAAAA-AAATATACAAAAAAAT
*
3876835 AATACAAAATACCAAAAAATATACAAAAAAAT
1 AATACAAAATACAAAAAAATATACAAAAAAAT
* *
3876867 AATAAAAAATAGAACAAAAA
1 AATACAAAATACAA-AAAAA
3876887 AAAAATCAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 8 0.18
32 31 0.70
33 5 0.11
ACGTcount: A:0.71, C:0.11, G:0.04, T:0.14
Consensus pattern (32 bp):
AATACAAAATACAAAAAAATATACAAAAAAAT
Found at i:3876864 original size:11 final size:11
Alignment explanation
Indices: 3876786--3876887 Score: 50
Period size: 11 Copynumber: 8.9 Consensus size: 11
3876776 AAAATACGAA
*
3876786 ATACAAAAAAC
1 ATACAAAAAAT
*
3876797 ATACAAAATACGAA
1 ATACAAAA-A--AT
3876811 ATACAAAAGAAAT
1 ATAC-AAA-AAAT
*
3876824 ATACCAAAAAT
1 ATACAAAAAAT
3876835 AATAC--AAAAT
1 -ATACAAAAAAT
*
3876845 A-CCAAAAAAT
1 ATACAAAAAAT
3876855 ATACAAAAAA-
1 ATACAAAAAAT
*
3876865 ATAATAAAAAAT
1 AT-ACAAAAAAT
*
3876877 AGAACAAAAAA
1 A-TACAAAAAA
3876888 AAAATCAAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 23
0.70 0.08 0.23
Matches are distributed among these distances:
8 1 0.01
9 1 0.01
10 13 0.18
11 26 0.37
12 15 0.21
13 5 0.07
14 5 0.07
15 4 0.06
16 1 0.01
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.14
Consensus pattern (11 bp):
ATACAAAAAAT
Found at i:3876970 original size:29 final size:29
Alignment explanation
Indices: 3876928--3877004 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
3876918 AACACCACTG
* * * *
3876928 CCACCAGGCACTACACCCTACCCTTCTGA
1 CCACCATGCCCTACACCCCACCCCTCTGA
3876957 CCACCATGCCCTAC-CCTCCACCCCTCTGA
1 CCACCATGCCCTACACC-CCACCCCTCTGA
* *
3876986 CTACCATGCCTTACCACCC
1 CCACCATGCCCTA-CACCC
3877005 ATTCTCTACC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.05
29 33 0.85
30 2 0.05
31 2 0.05
ACGTcount: A:0.21, C:0.53, G:0.08, T:0.18
Consensus pattern (29 bp):
CCACCATGCCCTACACCCCACCCCTCTGA
Found at i:3877198 original size:24 final size:24
Alignment explanation
Indices: 3877171--3877224 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3877161 ACAGAGAAGT
*
3877171 AAACATTGCAAAAA-AAAATAAAAA
1 AAACACTGCAAAAACAAAA-AAAAA
* *
3877195 AAACACTGTAAAAACTAAAAAAAA
1 AAACACTGCAAAAACAAAAAAAAA
3877219 AAACAC
1 AAACAC
3877225 AGTCCTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.72, C:0.13, G:0.04, T:0.11
Consensus pattern (24 bp):
AAACACTGCAAAAACAAAAAAAAA
Found at i:3883138 original size:666 final size:659
Alignment explanation
Indices: 3881940--3883263 Score: 2303
Period size: 666 Copynumber: 2.0 Consensus size: 659
3881930 ATTTGGCACC
3881940 ATATTGTCCAAAGATGAATGGGGCAGTAAAGGCTACAAATAAGAATATCAAAAGAATCCTAAAGA
1 ATATTGTCCAAAGATGAATGGGGCAGTAAAGGCTACAAATAAGAATATCAAAAGAATCCTAAAGA
*
3882005 AAATGACTGATACTTATAAAGATTGGCATGAAAAGTTATCTTTTGCTTTGCATACTTATAGAACA
66 AAATGACTGATACTTATAAAGATTGACATGAAAAGTTATCTTTTGCTTTGCATACTTATAGAACA
* * *
3882070 TCAGTCTGAACATCTATGGGGCCACTCCATTCTCTTTGGTATATGGAATGGAAGCTGTGCTACCA
131 TCAGTCCGAACATCTATGGGGCCACTCCATTCTCTTTGGTATATGGAATGAAAGCTGTACTACCA
*
3882135 ATCGAAGTAAAAATTCTCTCGTTGAGAGTCTTGATGGAGGTAGAATTAGAGGAAGTAGAATGGGT
196 ATCGAAGTAAAAATTCTCTCGCTGAGAGTCTTGATGGAGGTAGAATTAGAGGAAGTAGAATGGGT
*
3882200 TCGAAATTGCTACGAGCAGTTGAACCTCATTGAAGAGAAAAGACTTACAGCTCTTTGTCATGGTC
261 TCGAAATTGCTACGAGCAGTTGAACCTCATTGAAGAGAAAAGACTTACAGCACTTTGTCATGGTC
* *
3882265 AATTACATCAAAAGAGAATGATGAGAGCACATGACAAGAAAATTCATCCTCATTGCTTTACGAAA
326 AATTACATCAAAAGAGAATGATGAGAGCACATGACAAAAAAATCCATCCTCATTGCTTTACGAAA
*
3882330 GGAGATTTAGTGTTGAAAAAGATCCTTTCAAATCAACATGATAATCGAGAAAAATGGACACCAAA
391 GGAGATTTAGTGCTGAAAAAGATCCTTTCAAATCAACATGATAATCGAGAAAAATGGACACCAAA
* * *
3882395 TTGGAAAGGCCTGTATGTGGTGAAAAAGGCCTTTTCTGGTAGGGCATTGATTTTGACAGAAATGG
456 TTGGAAAGGCCCGTATGTGGTGAAAAAAGCCTTTTCTGGTAGGGCATTGATTTTGACAAAAATGG
* *
3882460 ATGGAAGTGATTTATCTGTT-TCGATAAATTCAGATACTGTGAAAAAATATTTTGCTTAAAAGAA
521 ACGGAAGTGATTTACCTGTTCT-GATAAATTCAGATACTGTGAAAAAATATTTTGCTT------A
*
3882524 AAAAAAAGTAAAAAATGAAAAATAATGATTCATCTAAGCTGAAAACCTGAAAAGACGGCTTGGAT
579 AAAAAAAGTAAAAAATGAAAAATAATGACTCATCTAAGCTGAAAACCTGAAAAGACGGCTTGGAT
3882589 GTGAAGAAGAAGCATT
644 GTGAAGAAGAAGCATT
* *
3882605 ATATTGTCTAAAGATGAATGGGGCAGTAAAGGCTGCAAATAAGAATATCAAAAGAATCCTAGAA-
1 ATATTGTCCAAAGATGAATGGGGCAGTAAAGGCTACAAATAAGAATATCAAAAGAATCCTA-AAG
3882669 AAAATGACTGATACTTATAAAGATTGACATGAAAAGTTATCTTTTGCTTTGCATACTTATAGAAC
65 AAAATGACTGATACTTATAAAGATTGACATGAAAAGTTATCTTTTGCTTTGCATACTTATAGAAC
*
3882734 ATCAGTCCGAACATCTATTGGGGCCACTCCATTTTCTTTGGTATATGGAATGAAAGCTGTACTAC
130 ATCAGTCCGAACATCTA-TGGGGCCACTCCATTCTCTTTGGTATATGGAATGAAAGCTGTACTAC
3882799 CAATCGAAGTAAAAATTCTCTCGCTGAGAGTCTTGATGGAGGTAGAATTAGAGGAAGTAGAATGG
194 CAATCGAAGTAAAAATTCTCTCGCTGAGAGTCTTGATGGAGGTAGAATTAGAGGAAGTAGAATGG
* *
3882864 GTTTGAAATTGCTACGAGCAGTTGAACCTCATTGAAGAGAAAAGACTTATAGCACTTTGTCATGG
259 GTTCGAAATTGCTACGAGCAGTTGAACCTCATTGAAGAGAAAAGACTTACAGCACTTTGTCATGG
* * *
3882929 TCAATTATATCAAAAGAGAATGATGAGAGCACATGACAAAAAAATCCGTCC-CTGTTGCTTTACG
324 TCAATTACATCAAAAGAGAATGATGAGAGCACATGACAAAAAAATCCATCCTC-ATTGCTTTACG
3882993 AAAGGAGATTTAGTGCTGAAAAAGATCCTTTCAAATCAACATGATAATCGAGAAAAATGGACACC
388 AAAGGAGATTTAGTGCTGAAAAAGATCCTTTCAAATCAACATGATAATCGAGAAAAATGGACACC
*
3883058 AAATTGGAAAGGCCCGTATGTGGTGAAAAAAGCCTTTTCTGGTGGGGCATTGATTTTGACAAAAA
453 AAATTGGAAAGGCCCGTATGTGGTGAAAAAAGCCTTTTCTGGTAGGGCATTGATTTTGACAAAAA
* *
3883123 TGGACGGAAGTGATTTACCTGTTCTGATAAATTTAGATATTGTGAAAAAATATTTTGCTTAAAAA
518 TGGACGGAAGTGATTTACCTGTTCTGATAAATTCAGATACTGTGAAAAAATATTTTGCTTAAAAA
3883188 AAAGTAAAAAATGAAAAATAATGACTCATCTAAGCTGAAAACCTGAAAAGACGGCTTGGATGTGA
583 AAAGTAAAAAATGAAAAATAATGACTCATCTAAGCTGAAAACCTGAAAAGACGGCTTGGATGTGA
3883253 AGAAGAAGCAT
648 AGAAGAAGCAT
3883264 CATTCCATAA
Statistics
Matches: 629, Mismatches: 26, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
660 80 0.13
665 140 0.22
666 408 0.65
667 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (659 bp):
ATATTGTCCAAAGATGAATGGGGCAGTAAAGGCTACAAATAAGAATATCAAAAGAATCCTAAAGA
AAATGACTGATACTTATAAAGATTGACATGAAAAGTTATCTTTTGCTTTGCATACTTATAGAACA
TCAGTCCGAACATCTATGGGGCCACTCCATTCTCTTTGGTATATGGAATGAAAGCTGTACTACCA
ATCGAAGTAAAAATTCTCTCGCTGAGAGTCTTGATGGAGGTAGAATTAGAGGAAGTAGAATGGGT
TCGAAATTGCTACGAGCAGTTGAACCTCATTGAAGAGAAAAGACTTACAGCACTTTGTCATGGTC
AATTACATCAAAAGAGAATGATGAGAGCACATGACAAAAAAATCCATCCTCATTGCTTTACGAAA
GGAGATTTAGTGCTGAAAAAGATCCTTTCAAATCAACATGATAATCGAGAAAAATGGACACCAAA
TTGGAAAGGCCCGTATGTGGTGAAAAAAGCCTTTTCTGGTAGGGCATTGATTTTGACAAAAATGG
ACGGAAGTGATTTACCTGTTCTGATAAATTCAGATACTGTGAAAAAATATTTTGCTTAAAAAAAA
GTAAAAAATGAAAAATAATGACTCATCTAAGCTGAAAACCTGAAAAGACGGCTTGGATGTGAAGA
AGAAGCATT
Found at i:3883997 original size:49 final size:48
Alignment explanation
Indices: 3883926--3884739 Score: 733
Period size: 48 Copynumber: 17.0 Consensus size: 48
3883916 GTTTTGAGAA
* ** * * * *
3883926 AAGATGAGATTTTAAAGTTGTTGAGTTTTTACTGAAAGGAGCTTTTAC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
*
3883974 AAGATAAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTC
1 AAGATAAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * *
3884023 ---ATGAGATTTTAAAGTTATTGAGCCTCTACTGAGATGAGCTTTTTC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
3884068 AA-ATGAA-ATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCATTTTC
1 AAGAT-AAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
* ** * * *
3884117 AAGAT--GACTTTAAAGTCATTGAGCATCTACTGAGATGAGCCATTTTTC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-C-TTTTTC
* * *
3884165 AA-ATGAGATTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCCTTTTC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
* * * *
3884213 AAGATGA-ATTTTAAAGTCGTTAAGCCTCTGCTGAGAGGAGCCCTTTTC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
* * * *
3884261 TAA-ATGAGATTTTAAAGTTGTTGAGCCTCTGCTAAGAGAAGCCCTTTTC
1 -AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
* * * *
3884310 AAGATGA-ATTTTAAAGTTGTTAAGCCTTTG-TCGAGAAGAGCTTTTTC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCT-GAGAGGAGCTTTTTC
* * *
3884357 -AGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGGGTTTTTTC
1 AAGATAAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
3884405 -----AAGATTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCTTTTCC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * * *
3884448 AAGATAAAATTTTAAAGTTGTTAAGCCTTTGTTGAGAGAAGATTTTTC
1 AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
*
3884496 -AGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
1 AAGATAAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
3884544 AA-A-AGAGATTTTAAAGTCGTTGAGCTTCTACTGAGAGGAGCTTTTTCC
1 AAGATA-AGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-C
* * * *
3884592 AA-A-AGAGATTTTAAAGTCGTTGAGCCTCTACTGAGATGAGTTTTTTCC
1 AAGATA-AGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT-C
* * *
3884640 AAGATGAA-ATTTTTAAAGTCGTTGAGCCTCTGCTGAAAGGAGCTTTTCC
1 AAGAT-AAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
*
3884689 AAGATGAA-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGTCTTTTTC
1 AAGAT-AAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
3884739 A
1 A
3884740 GATTTTAAAT
Statistics
Matches: 648, Mismatches: 85, Indels: 64
0.81 0.11 0.08
Matches are distributed among these distances:
43 35 0.05
44 3 0.00
45 35 0.05
46 11 0.02
47 82 0.13
48 275 0.42
49 163 0.25
50 43 0.07
51 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (48 bp):
AAGATAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
Found at i:3884970 original size:7 final size:7
Alignment explanation
Indices: 3884958--3885015 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
3884948 TTTTTTTAAA
3884958 AAAATAC
1 AAAATAC
3884965 AAAATAC
1 AAAATAC
*
3884972 GAAATAC
1 AAAATAC
*
3884979 AAAAGA-
1 AAAATAC
*
3884985 AATATAC
1 AAAATAC
3884992 AAAA-A-
1 AAAATAC
*
3884997 ATAATAC
1 AAAATAC
3885004 AAAATACC
1 AAAATA-C
3885012 AAAA
1 AAAA
3885016 AATATAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
5 3 0.08
6 6 0.15
7 25 0.64
8 5 0.13
ACGTcount: A:0.71, C:0.12, G:0.03, T:0.14
Consensus pattern (7 bp):
AAAATAC
Found at i:3885033 original size:33 final size:34
Alignment explanation
Indices: 3884954--3885052 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 34
3884944 AAAATTTTTT
* *
3884954 TAAAAAAATACAAAATACGAAATACAAAAGAAATA
1 TAAAAAAATA-ATAATACAAAATACAAAAGAAATA
* *
3884989 T-ACAAAA-AATAATACAAAATACCAAA-AAATA
1 TAAAAAAATAATAATACAAAATACAAAAGAAATA
* *
3885020 TAAAAAAATAATAATAAAAAATAAAACAAGAAA
1 TAAAAAAATAATAATACAAAATACAA-AAGAAA
3885053 AAAGAAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
31 6 0.12
32 20 0.38
33 15 0.29
34 7 0.13
35 4 0.08
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (34 bp):
TAAAAAAATAATAATACAAAATACAAAAGAAATA
Found at i:3887424 original size:20 final size:20
Alignment explanation
Indices: 3887385--3887421 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3887375 TTTTAGAAAT
*
3887385 TTTATTAATTGTTTTATTAA
1 TTTATTAATTGTTTAATTAA
3887405 TTTATTAATT-TTTAATT
1 TTTATTAATTGTTTAATT
3887422 TAAATTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTATTAATTGTTTAATTAA
Found at i:3887832 original size:17 final size:17
Alignment explanation
Indices: 3887791--3887833 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3887781 TTTTTTCTTA
* *
3887791 TTTTTTATTAATTTTGT
1 TTTTTTATTAAGTTTAT
* *
3887808 ATTATTATTAAGTTTAT
1 TTTTTTATTAAGTTTAT
3887825 TTTTTTATT
1 TTTTTTATT
3887834 TTTAAAGTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTTTTATTAAGTTTAT
Found at i:3887838 original size:20 final size:21
Alignment explanation
Indices: 3887782--3887848 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
3887772 AAAAGCTTTT
* * *
3887782 TTTTTCTTATTTTTTA-TTAA
1 TTTTTATTATTTTTAAGTTTA
*
3887802 TTTTGTATTATTATTAAGTTTA
1 TTTT-TATTATTTTTAAGTTTA
3887824 TTTTT-TTATTTTTAAAGTTTA
1 TTTTTATTATTTTT-AAGTTTA
3887845 TTTT
1 TTTT
3887849 AAAAATTAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.28
21 21 0.54
22 7 0.18
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTTATTATTTTTAAGTTTA
Found at i:3888701 original size:23 final size:23
Alignment explanation
Indices: 3888675--3888718 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3888665 GAGCTTTTTG
* *
3888675 GGATTCAAATCTTAGATTTTCTA
1 GGATTCAAATCTCAAATTTTCTA
3888698 GGATTCAAATCTCAAATTTTC
1 GGATTCAAATCTCAAATTTTC
3888719 AACCCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (23 bp):
GGATTCAAATCTCAAATTTTCTA
Found at i:3888870 original size:16 final size:15
Alignment explanation
Indices: 3888849--3888903 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
3888839 TTAGATAAGG
3888849 AAAGAAGAAGAATGAA
1 AAAGAA-AAGAATGAA
3888865 AAAG-AAAGAA--AA
1 AAAGAAAAGAATGAA
*
3888877 AAAGAAAAAAATAGAA
1 AAAGAAAAGAAT-GAA
3888893 AAAG-AAAGAAT
1 AAAGAAAAGAAT
3888904 AGAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
14 5 0.15
15 7 0.21
16 10 0.30
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.05
Consensus pattern (15 bp):
AAAGAAAAGAATGAA
Found at i:3888875 original size:10 final size:10
Alignment explanation
Indices: 3888848--3888902 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
3888838 ATTAGATAAG
*
3888848 GAAAGAAGAA
1 GAAAGAAAAA
*
3888858 GAATGAAAAA
1 GAAAGAAAAA
3888868 GAAAG-AAAA
1 GAAAGAAAAA
3888877 -AAAGAAAAA
1 GAAAGAAAAA
3888886 -AATAGAAAAA
1 GAA-AGAAAAA
3888896 GAAAGAA
1 GAAAGAA
3888903 TAGAATAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
8 4 0.10
9 10 0.26
10 23 0.59
11 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (10 bp):
GAAAGAAAAA
Found at i:3888893 original size:28 final size:28
Alignment explanation
Indices: 3888849--3888902 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
3888839 TTAGATAAGG
*
3888849 AAAGAAGAAGAATGAAAAAGAAAGAAAA
1 AAAGAAGAAAAATGAAAAAGAAAGAAAA
3888877 AAAGAA-AAAAATAGAAAAAGAAAGAA
1 AAAGAAGAAAAAT-GAAAAAGAAAGAA
3888903 TAGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (28 bp):
AAAGAAGAAAAATGAAAAAGAAAGAAAA
Found at i:3889172 original size:49 final size:49
Alignment explanation
Indices: 3889118--3889245 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 49
3889108 CTCCTATGAG
* *
3889118 CAGAGGCTCAACAACTTTAAAATTCTCATTTTG-GAAAAGCTCT-TCTCAA
1 CAGAGGCTCAACAACTTTAAAA-TCTCATCTTGAAAAAAG-TCTATCTCAA
* * * *
3889167 CAGAGGCTCAACAATTTTAAAAATCTTATCTTGAAAAAAAGTTTATCTCAG
1 CAGAGGCTCAACAACTTT-AAAATCTCATCTTG-AAAAAAGTCTATCTCAA
* *
3889218 TAGAGGCACAACAACTTTAAAATCTCAT
1 CAGAGGCTCAACAACTTTAAAATCTCAT
3889246 ATGTTCTCGA
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
49 25 0.38
50 15 0.23
51 25 0.38
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (49 bp):
CAGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAAGTCTATCTCAA
Found at i:3897680 original size:20 final size:20
Alignment explanation
Indices: 3897655--3897713 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
3897645 CAGGTCCGGG
3897655 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
3897675 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
3897695 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
3897714 GCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:3897762 original size:7 final size:7
Alignment explanation
Indices: 3897750--3897783 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
3897740 TTTTTACCCG
3897750 TATTTTT
1 TATTTTT
3897757 TATTTTT
1 TATTTTT
3897764 TA-TTTT
1 TATTTTT
3897770 TA-TTTT
1 TATTTTT
3897776 TATTTTT
1 TATTTTT
3897783 T
1 T
3897784 TCTTTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:3897769 original size:6 final size:6
Alignment explanation
Indices: 3897753--3897782 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3897743 TTACCCGTAT
3897753 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTT
3897783 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:3898033 original size:11 final size:12
Alignment explanation
Indices: 3898013--3898045 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3898003 ATCTAGATTT
*
3898013 TTTTTTTTTTAA
1 TTTTTATTTTAA
3898025 -TTTTATTTTAA
1 TTTTTATTTTAA
3898036 TTTTTATTTT
1 TTTTTATTTT
3898046 GGAGGGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTTAA
Found at i:3898397 original size:31 final size:31
Alignment explanation
Indices: 3898362--3898432 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
3898352 AATTTCCAGA
* *
3898362 TTCCGGCGAAAATTCTGGCG-ACTTTTGAATT
1 TTCCGGCGAAAATTCCGGCGAAC-TTTGAAGT
* *
3898393 TTCCGGTGACAATTCCGGCGAACTTTGAAGT
1 TTCCGGCGAAAATTCCGGCGAACTTTGAAGT
3898424 TTCCGGCGA
1 TTCCGGCGA
3898433 CAGACCCAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (31 bp):
TTCCGGCGAAAATTCCGGCGAACTTTGAAGT
Found at i:3898526 original size:19 final size:19
Alignment explanation
Indices: 3898502--3898538 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3898492 CAATTTTCGG
*
3898502 CGAAATTCCCAGATTCCGA
1 CGAAATTCCCAGAATCCGA
*
3898521 CGAAATTTCCAGAATCCG
1 CGAAATTCCCAGAATCCG
3898539 GCACCGGCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
CGAAATTCCCAGAATCCGA
Found at i:3898774 original size:5 final size:5
Alignment explanation
Indices: 3898760--3898802 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
3898750 TTCAGCCCCT
* *
3898760 CCGAG CCGAG TCGAG CCGAG CCGAG CCGCA- CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCG-AG CCGAG CCGAG CCG
3898803 CGATCCGAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.03
5 30 0.94
6 1 0.03
ACGTcount: A:0.21, C:0.42, G:0.35, T:0.02
Consensus pattern (5 bp):
CCGAG
Found at i:3898868 original size:1 final size:1
Alignment explanation
Indices: 3898822--3898848 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3898812 CCGCTCCAGG
3898822 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3898849 GAATTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3898873 original size:10 final size:10
Alignment explanation
Indices: 3898822--3898873 Score: 54
Period size: 9 Copynumber: 5.3 Consensus size: 10
3898812 CCGCTCCAGG
3898822 TTTTTTTTT-
1 TTTTTTTTTA
3898831 TTTTTTTTT-
1 TTTTTTTTTA
3898840 TTTTTTTTTGA
1 TTTTTTTTT-A
* **
3898851 ATTTTTTGAA
1 TTTTTTTTTA
3898861 TTTTTTTTTA
1 TTTTTTTTTA
3898871 TTT
1 TTT
3898874 GACTTTGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
9 18 0.51
10 11 0.31
11 6 0.17
ACGTcount: A:0.10, C:0.00, G:0.04, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:3899157 original size:161 final size:161
Alignment explanation
Indices: 3898891--3899349 Score: 768
Period size: 156 Copynumber: 2.9 Consensus size: 161
3898881 ATTTTGATCT
* * *
3898891 TGATTTT-TTTTTCTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAG
1 TGATTTTGATTTT-TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAG
*
3898955 TTTTTCTTGCATACTCCTGAGGTGAGAGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAA
64 TTTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAA
*
3899020 TTGAGAATAATTTCCGATAATTAATTACTTGGC
129 TTGAGAATAATTTCCGATAATTAATTAATTGGC
3899053 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
3899118 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
66 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
* *
3899183 GAGAATAATTTTCGATAATTAATTAATTGGT
131 GAGAATAATTTCCGATAATTAATTAATTGGC
* *
3899214 TGATCTTGA-----TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
*
3899274 TTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
66 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
3899339 GAGAATAATTT
131 GAGAATAATTT
3899350 TCAACAACTA
Statistics
Matches: 286, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
156 125 0.44
161 111 0.39
162 46 0.16
163 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (161 bp):
TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
GAGAATAATTTCCGATAATTAATTAATTGGC
Found at i:3902599 original size:1 final size:1
Alignment explanation
Indices: 3902595--3902620 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3902585 GTAATTTTTG
3902595 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3902621 CCACAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3903034 original size:21 final size:21
Alignment explanation
Indices: 3903010--3903057 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3903000 AAAAATGATA
*
3903010 AAAAAAAAAAAGGGAAAAATG
1 AAAAAAAAAAAGGAAAAAATG
*
3903031 AAAAAAAAGAAGGAAAAAATG
1 AAAAAAAAAAAGGAAAAAATG
*
3903052 AGAAAA
1 AAAAAA
3903058 TGAAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAAGGAAAAAATG
Found at i:3904404 original size:41 final size:41
Alignment explanation
Indices: 3904295--3904648 Score: 357
Period size: 41 Copynumber: 8.4 Consensus size: 41
3904285 GTCTAGGAGT
* *
3904295 ATTTACTTTTCCAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
* * *
3904335 ATTTACTTTTCAAAAGTCGTGTTGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTTC-AAAGTCGTGGTACCTCTGTTTAGAGGAGCA
3904377 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
* *
3904418 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
3904460 ATTTACTTTTCAAAGTCGTGCCTTAGGGAATACCAAGTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTC--G---T--GG--TACC---TCTGTTTAGAGGAGCA
*
3904513 ATTTATTTTTCCAAAGTCGTGGTACCTCTG-TTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
*
3904554 ATTTACTTTTCAAAGTTCGT--T-GCTCTGTTCTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGGTACCTCTGTT-TAGAGGAGCA
* * *
3904594 ATTTATTTTTCAAAAAT-GT-GTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTC-AAAGTCGTGGTACCTCTGTTTAGAGGAGCA
*
3904634 ATTT-TTTTTCAAAGT
1 ATTTACTTTTCAAAGT
3904649 AAGTGCCTCG
Statistics
Matches: 274, Mismatches: 17, Indels: 48
0.81 0.05 0.14
Matches are distributed among these distances:
38 9 0.03
39 10 0.04
40 55 0.20
41 80 0.29
42 73 0.27
43 1 0.00
45 4 0.01
46 1 0.00
47 2 0.01
48 2 0.01
49 1 0.00
50 4 0.01
52 1 0.00
53 24 0.09
54 7 0.03
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (41 bp):
ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
Found at i:3904479 original size:83 final size:81
Alignment explanation
Indices: 3904295--3904478 Score: 287
Period size: 83 Copynumber: 2.2 Consensus size: 81
3904285 GTCTAGGAGT
* * * * *
3904295 ATTTACTTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGTTGC
1 ATTTACTTTTCAAAG-TCGTTACCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTCGTGGTAC
3904360 CTCTGTTGAGAGGAGCA
65 CTCTGTTGAGAGGAGCA
*
3904377 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTA
1 ATTTACTTTTCAAAGTCGT--TACCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTCGTGGTA
3904442 CCTCTGTTGAGAGGAGCA
64 CCTCTGTTGAGAGGAGCA
3904460 ATTTACTTTTCAAAGTCGT
1 ATTTACTTTTCAAAGTCGT
3904479 GCCTTAGGGA
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
81 4 0.04
82 14 0.15
83 76 0.81
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (81 bp):
ATTTACTTTTCAAAGTCGTTACCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTCGTGGTACC
TCTGTTGAGAGGAGCA
Found at i:3904588 original size:40 final size:40
Alignment explanation
Indices: 3904497--3904648 Score: 188
Period size: 40 Copynumber: 3.8 Consensus size: 40
3904487 GAATACCAAG
3904497 TCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACC
1 TCTGTTTAGAGGAGCAATTTATTTTT-CAAAGTCGT-GTACC
* *
3904539 TCTG-TTAGAGGAGCAATTTACTTTTCAAAGTTCGT-T-GC
1 TCTGTTTAGAGGAGCAATTTATTTTTCAAAG-TCGTGTACC
*
3904577 TCTGTTCTAGAGGAGCAATTTATTTTTCAAAAAT-GTGTACC
1 TCTGTT-TAGAGGAGCAATTTATTTTTC-AAAGTCGTGTACC
*
3904618 TCTGTTGAGAGGAGCAATTT-TTTTTCAAAGT
1 TCTGTTTAGAGGAGCAATTTATTTTTCAAAGT
3904649 AAGTGCCTCG
Statistics
Matches: 97, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
38 9 0.09
39 10 0.10
40 40 0.41
41 34 0.35
42 4 0.04
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.39
Consensus pattern (40 bp):
TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGTACC
Found at i:3904666 original size:38 final size:39
Alignment explanation
Indices: 3904497--3904666 Score: 147
Period size: 40 Copynumber: 4.3 Consensus size: 39
3904487 GAATACCAAG
* *
3904497 TCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT-CGTGGTACC
1 TCTGTTGAGAGGAGCAATTTATTTTT-CAAAGTAAGT-G--CC
* **
3904539 TCTGTT-AGAGGAGCAATTTACTTTTCAAAGTTCGTTG-C
1 TCTGTTGAGAGGAGCAATTTATTTTTCAAAGTAAG-TGCC
*
3904577 TCTGTTCTAGAGGAGCAATTTATTTTTCAAA--AATGTGTACC
1 TCTGTT-GAGAGGAGCAATTTATTTTTCAAAGTAA-GTG--CC
3904618 TCTGTTGAGAGGAGCAATTT-TTTTTCAAAGTAAGTGCC
1 TCTGTTGAGAGGAGCAATTTATTTTTCAAAGTAAGTGCC
3904656 TC-GTTAGAGAG
1 TCTGTT-GAGAG
3904667 CATTATCAAA
Statistics
Matches: 112, Mismatches: 5, Indels: 26
0.78 0.03 0.18
Matches are distributed among these distances:
37 3 0.03
38 18 0.16
39 10 0.09
40 44 0.39
41 30 0.27
42 7 0.06
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (39 bp):
TCTGTTGAGAGGAGCAATTTATTTTTCAAAGTAAGTGCC
Found at i:3904953 original size:20 final size:20
Alignment explanation
Indices: 3904928--3904986 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
3904918 CAGGTCCGGG
3904928 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
3904948 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
3904968 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
3904987 GCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:3905036 original size:7 final size:7
Alignment explanation
Indices: 3905024--3905057 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
3905014 TTTTACCCCG
3905024 TATTTTT
1 TATTTTT
3905031 TATTTTT
1 TATTTTT
3905038 TA-TTTT
1 TATTTTT
3905044 TA-TTTT
1 TATTTTT
3905050 TATTTTT
1 TATTTTT
3905057 T
1 T
3905058 TCTTTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:3905043 original size:6 final size:6
Alignment explanation
Indices: 3905027--3905056 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3905017 TACCCCGTAT
3905027 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTT
3905057 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:3905308 original size:11 final size:12
Alignment explanation
Indices: 3905288--3905320 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3905278 ATCTAGATTT
*
3905288 TTTTTTTTTTAA
1 TTTTTATTTTAA
3905300 -TTTTATTTTAA
1 TTTTTATTTTAA
3905311 TTTTTATTTT
1 TTTTTATTTT
3905321 GGAGGGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTTAA
Found at i:3905709 original size:31 final size:31
Alignment explanation
Indices: 3905637--3905709 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
3905627 AATTTCCAGA
* *
3905637 TTCCGACGAAAATTCCGGCGACTTTTGAATT
1 TTCCGACGACAATTCCGGCGACTTTTGAAGT
*
3905668 TTCCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGACGACAATTCCGGCG-ACTTTTGAAGT
3905699 TTCCGACGACA
1 TTCCGACGACA
3905710 GACCCAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (31 bp):
TTCCGACGACAATTCCGGCGACTTTTGAAGT
Found at i:3905795 original size:19 final size:19
Alignment explanation
Indices: 3905771--3905815 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3905761 TCCGACCAAT
3905771 TTCCGGCGAAA-TTCTCAGA
1 TTCCGGCGAAATTTC-CAGA
3905790 TTCCGGCGAAATTTCCAGA
1 TTCCGGCGAAATTTCCAGA
*
3905809 ATCCGGC
1 TTCCGGC
3905816 ACCGGCGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (19 bp):
TTCCGGCGAAATTTCCAGA
Found at i:3906100 original size:9 final size:9
Alignment explanation
Indices: 3906088--3906120 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
3906078 TTTTTTTTTT
3906088 TTTTTTGAA
1 TTTTTTGAA
3906097 TTTTTTGAA
1 TTTTTTGAA
3906106 TTTTTTGAA
1 TTTTTTGAA
3906115 TTTTTT
1 TTTTTT
3906121 TTTATTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:3906102 original size:18 final size:18
Alignment explanation
Indices: 3906079--3906123 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3906069 GCTCCAGGTT
3906079 TTTTTTTTTTTTTTTGAA
1 TTTTTTTTTTTTTTTGAA
***
3906097 TTTTTTGAATTTTTTGAA
1 TTTTTTTTTTTTTTTGAA
3906115 TTTTTTTTT
1 TTTTTTTTT
3906124 ATTTGACTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTGAA
Found at i:3906623 original size:156 final size:157
Alignment explanation
Indices: 3906159--3906623 Score: 770
Period size: 156 Copynumber: 2.9 Consensus size: 157
3906149 TTTTTTTTTC
* *
3906159 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATAC
1 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATAC
*
3906224 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTC
65 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTT
* *
3906289 CGATAATTAATTACTTGGCTGATTTTGA
130 CGATAATTAATTACTTGGTTGATCTTGA
*
3906317 TTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTTTGCAAGTGAAACAGTAGTTTTTCTTGCAT
1 ---TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCAT
3906382 ACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATT
63 ACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATT
*
3906447 TTCGATAATTAATTAATTGGTTGATCTTGA
128 TTCGATAATTAATTACTTGGTTGATCTTGA
*
3906477 -TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACT
1 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACT
*
3906541 CTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
* * * *
3906606 AACAACTAACTACTTGGT
131 GATAATTAATTACTTGGT
3906624 AAAATTTTAA
Statistics
Matches: 289, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
156 139 0.48
160 112 0.39
161 38 0.13
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (157 bp):
TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACT
CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
GATAATTAATTACTTGGTTGATCTTGA
Found at i:3909637 original size:3 final size:3
Alignment explanation
Indices: 3909572--3909618 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3909562 ATATATACAA
3909572 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3909619 AGCATAAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3911891 original size:1 final size:1
Alignment explanation
Indices: 3911881--3911938 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
3911871 AGGAAGAAGG
* * * * * * *
3911881 AAAAATAAAAAAAATAAAAAAAATAAAAAAATAAAAAAAGAAAGAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3911939 TGATAATAAA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (1 bp):
A
Found at i:3911895 original size:9 final size:9
Alignment explanation
Indices: 3911881--3911939 Score: 86
Period size: 9 Copynumber: 6.7 Consensus size: 9
3911871 AGGAAGAAGG
3911881 AAAAATAAA
1 AAAAATAAA
3911890 AAAAATAAA
1 AAAAATAAA
3911899 AAAAAT-AA
1 AAAAATAAA
3911907 AAAAATAAA
1 AAAAATAAA
*
3911916 AAAAGA-AAG
1 AAAA-ATAAA
3911925 AAAAATAAA
1 AAAAATAAA
3911934 AAAAAT
1 AAAAAT
3911940 GATAATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 9 0.20
9 35 0.78
10 1 0.02
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:3911915 original size:26 final size:26
Alignment explanation
Indices: 3911881--3911937 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
3911871 AGGAAGAAGG
3911881 AAAAATAAAAAAA-ATAAAAAAAATAA
1 AAAAATAAAAAAAGA-AAAAAAAATAA
*
3911907 AAAAATAAAAAAAGAAAGAAAAATAA
1 AAAAATAAAAAAAGAAAAAAAAATAA
3911933 AAAAA
1 AAAAA
3911938 ATGATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.88, C:0.00, G:0.04, T:0.09
Consensus pattern (26 bp):
AAAAATAAAAAAAGAAAAAAAAATAA
Found at i:3913542 original size:13 final size:13
Alignment explanation
Indices: 3913503--3913544 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3913493 ATTTTATATA
*
3913503 TAATATATTAATG
1 TAATATATTAATT
3913516 TAAT-TATT-ATT
1 TAATATATTAATT
*
3913527 TAATACATTAATT
1 TAATATATTAATT
3913540 TAATA
1 TAATA
3913545 AAATATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 7 0.28
13 12 0.48
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (13 bp):
TAATATATTAATT
Found at i:3913697 original size:18 final size:18
Alignment explanation
Indices: 3913674--3913709 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3913664 TTATGTTTTT
* *
3913674 TTTTTTTTTTTTACTTTA
1 TTTTTTATTTTTAATTTA
3913692 TTTTTTATTTTTAATTTA
1 TTTTTTATTTTTAATTTA
3913710 AAAAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTATTTTTAATTTA
Found at i:3914156 original size:24 final size:25
Alignment explanation
Indices: 3914109--3914163 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3914099 TCTCTAGCCT
*
3914109 TTTTTTTTTTTTTTCATTTTCTTCA
1 TTTTTTTTTTTTTTCATTTCCTTCA
*
3914134 TTTTTTTTTTTTTT-GTTTCCTTCA
1 TTTTTTTTTTTTTTCATTTCCTTCA
*
3914158 TGTTTT
1 TTTTTT
3914164 CCATTTTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.05, C:0.11, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTTTTTTCATTTCCTTCA
Found at i:3914169 original size:33 final size:30
Alignment explanation
Indices: 3914108--3914170 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
3914098 GTCTCTAGCC
*
3914108 TTTTTTTTTTTTTTTCATTTTCTTCATTTT
1 TTTTTTTTTTTTTTTCATTTTCTCCATTTT
3914138 TTTTTTTTTTGTTTCCTTCATGTTT-TCCATTTT
1 TTTTTTTTTT-TTT--TTCAT-TTTCTCCATTTT
3914171 CCATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 10 0.36
31 3 0.11
33 12 0.43
34 3 0.11
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.78
Consensus pattern (30 bp):
TTTTTTTTTTTTTTTCATTTTCTCCATTTT
Found at i:3920718 original size:3 final size:3
Alignment explanation
Indices: 3920710--3920735 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3920700 AGCAATGAAA
3920710 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3920736 AGCTTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3921185 original size:11 final size:11
Alignment explanation
Indices: 3921169--3921195 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3921159 TATAAGAATG
3921169 AATTTTAAATA
1 AATTTTAAATA
3921180 AATTTTAAATA
1 AATTTTAAATA
3921191 AATTT
1 AATTT
3921196 ATTTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTTTAAATA
Found at i:3921701 original size:28 final size:29
Alignment explanation
Indices: 3921662--3921725 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
3921652 ATGTTTGATT
3921662 AATT-AATATTTAA-ATAATTTTATTA-AA
1 AATTAAATATTTAATA-AATTTTATTAGAA
* *
3921689 AATTAAATTTTTAATAAATTTTTTTAGAA
1 AATTAAATATTTAATAAATTTTATTAGAA
3921718 ATATTAAA
1 A-ATTAAA
3921726 AAAATTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 4 0.13
28 17 0.55
29 4 0.13
30 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
AATTAAATATTTAATAAATTTTATTAGAA
Found at i:3922579 original size:27 final size:28
Alignment explanation
Indices: 3922549--3922609 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
3922539 AGGAAGAAAG
3922549 AAAATAAAT-TAAAATAATAATAATAAT
1 AAAATAAATGTAAAATAATAATAATAAT
*
3922576 AAAACT--ATGTACAATAATAATAATAAT
1 AAAA-TAAATGTAAAATAATAATAATAAT
*
3922603 AATATAA
1 AAAATAA
3922610 CAATAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.11
27 24 0.86
28 1 0.04
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATAAATGTAAAATAATAATAATAAT
Found at i:3924777 original size:37 final size:38
Alignment explanation
Indices: 3924713--3924812 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 38
3924703 ATAGTTTAGG
* *
3924713 TAAATATGATAATTTGTATATT--TATTTTATGTAAAATAT
1 TAAATATCATAA-TT-TATATTAATATTTTATATAAAA-AT
3924752 TAAA-AT-ATATATTTATA-TAATATTTTATATAAAAAT
1 TAAATATCATA-ATTTATATTAATATTTTATATAAAAAT
*
3924788 TATATATCATAATTTATATTAATAT
1 TAAATATCATAATTTATATTAATAT
3924813 AAAAATAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
35 1 0.02
36 9 0.17
37 27 0.51
38 12 0.23
39 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (38 bp):
TAAATATCATAATTTATATTAATATTTTATATAAAAAT
Found at i:3925058 original size:20 final size:20
Alignment explanation
Indices: 3925033--3925072 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3925023 TGACTGAATG
*
3925033 CTCCTAATTGGATAAGCATA
1 CTCCTAATTAGATAAGCATA
3925053 CTCCTAATTAGATAAGCATA
1 CTCCTAATTAGATAAGCATA
3925073 TGTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (20 bp):
CTCCTAATTAGATAAGCATA
Found at i:3929733 original size:12 final size:13
Alignment explanation
Indices: 3929708--3929735 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3929698 GAATTCTTAA
3929708 TTTTTAAAATTTT
1 TTTTTAAAATTTT
3929721 TTTTTAAAATTTT
1 TTTTTAAAATTTT
3929734 TT
1 TT
3929736 AAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTAAAATTTT
Found at i:3929946 original size:3 final size:3
Alignment explanation
Indices: 3929938--3929977 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3929928 TTGAAAATCA
3929938 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3929978 TTGTTAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3934389 original size:20 final size:20
Alignment explanation
Indices: 3934364--3934401 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3934354 TTTTTATATA
3934364 ATCTATTTATCTATATATCT
1 ATCTATTTATCTATATATCT
* *
3934384 ATCTATTTGTTTATATAT
1 ATCTATTTATCTATATAT
3934402 AAAATTGTGA
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:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (20 bp):
ATCTATTTATCTATATATCT
Found at i:3935250 original size:2 final size:2
Alignment explanation
Indices: 3935243--3935271 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3935233 AAATCTTAAG
3935243 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
3935272 ACATATTTGT
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:3936303 original size:27 final size:26
Alignment explanation
Indices: 3936273--3936459 Score: 73
Period size: 26 Copynumber: 7.1 Consensus size: 26
3936263 AACTAATTTC
*
3936273 AAATTAAAAAATATGAAAATTTCTTAA
1 AAATTAAAAAATATAAAAATTT-TTAA
* * * *
3936300 AAATCATAAAATTTTAATAA-TTTTAA
1 AAATTA-AAAAATATAAAAATTTTTAA
* *
3936326 AAATTCAAAAAAAATTAAAAATTTGATAA
1 AAATT-AAAAAATA-TAAAAATTT-TTAA
* *
3936355 AAATCTAAAAAAT-TCAAGAAA--ATGAA
1 AAAT-TAAAAAATAT-AA-AAATTTTTAA
* *
3936381 AATTTTAATAAA-A-AAAAATTATTTAA
1 AA-ATTAAAAAATATAAAAATT-TTTAA
* * * *
3936407 AATTTAAAAAATTTTAAAATTTTAAA
1 AAATTAAAAAATATAAAAATTTTTAA
* * *
3936433 AAACT-AAAAATAAAAAAATTTTGAA
1 AAATTAAAAAATATAAAAATTTTTAA
3936458 AA
1 AA
3936460 TATTTGAAAA
Statistics
Matches: 116, Mismatches: 29, Indels: 32
0.66 0.16 0.18
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 26 0.22
26 34 0.29
27 21 0.18
28 13 0.11
29 16 0.14
30 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (26 bp):
AAATTAAAAAATATAAAAATTTTTAA
Found at i:3936336 original size:54 final size:53
Alignment explanation
Indices: 3936234--3936364 Score: 124
Period size: 54 Copynumber: 2.4 Consensus size: 53
3936224 AAGATTTCAT
* * * * *
3936234 AAAATTTTTTAAAAAATACAAAAAATTATAACTAATTTCAAATTAAAAAATA-TG
1 AAAATTTCTT-AAAAAT-CATAAAATTATAACTAATTTAAAATTAAAAAAAATTA
*
3936288 AAAATTTCTTAAAAATCATAAAATTTTAA-TAATTTTAAAAATTCAAAAAAAATTA
1 AAAATTTCTTAAAAATCATAAAATTATAACTAA-TTT-AAAATT-AAAAAAAATTA
**
3936343 AAAATTTGATAAAAATC-TAAAA
1 AAAATTTCTTAAAAATCATAAAA
3936365 AATTCAAGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 3 0.05
52 14 0.22
53 11 0.17
54 21 0.32
55 16 0.25
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (53 bp):
AAAATTTCTTAAAAATCATAAAATTATAACTAATTTAAAATTAAAAAAAATTA
Found at i:3936339 original size:37 final size:34
Alignment explanation
Indices: 3936298--3936391 Score: 89
Period size: 38 Copynumber: 2.6 Consensus size: 34
3936288 AAAATTTCTT
* *
3936298 AAAAATCATAAAATTTTAATAATTTTAAAAATTCAAA
1 AAAAAT-A-AAAATTTTAATAATCTAAAAAATTC-AA
*
3936335 AAAAATTAAAAATTTGATAAAAATCTAAAAAATTCAA
1 AAAAA-TAAAAATTT--TAATAATCTAAAAAATTCAA
* *
3936372 GAAAATGAAAATTTTAATAA
1 AAAAATAAAAATTTTAATAA
3936392 AAAAAAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
34 5 0.10
36 15 0.31
37 12 0.25
38 16 0.33
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (34 bp):
AAAAATAAAAATTTTAATAATCTAAAAAATTCAA
Found at i:3936343 original size:18 final size:18
Alignment explanation
Indices: 3936322--3936376 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3936312 TTTAATAATT
3936322 TTAAAAATTCAAAAAAAA
1 TTAAAAATTCAAAAAAAA
** *
3936340 TTAAAAATTTGATAAAAA
1 TTAAAAATTCAAAAAAAA
3936358 TCTAAAAAATTCAAGAAAA
1 T-T-AAAAATTCAA-AAAA
3936377 TGAAAATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 16 0.57
19 1 0.04
20 8 0.29
21 3 0.11
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.25
Consensus pattern (18 bp):
TTAAAAATTCAAAAAAAA
Found at i:3936422 original size:17 final size:18
Alignment explanation
Indices: 3936402--3936435 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3936392 AAAAAAATTA
3936402 TTTAAAA-TTTAAAAAAT
1 TTTAAAATTTTAAAAAAT
3936419 TTTAAAATTTTAAAAAA
1 TTTAAAATTTTAAAAAA
3936436 CTAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAAAATTTTAAAAAAT
Found at i:3936682 original size:31 final size:31
Alignment explanation
Indices: 3936627--3936702 Score: 113
Period size: 29 Copynumber: 2.5 Consensus size: 31
3936617 GAATACTTTA
3936627 TTTTATT-AAAATTTTTGTTTTTTA-TAATT
1 TTTTATTGAAAATTTTTGTTTTTTATTAATT
3936656 TTTT-TTGAAAATTTTTGGATTTTTTATTAATT
1 TTTTATTGAAAATTTTT-G-TTTTTTATTAATT
3936688 TTTTATTGAAAATTT
1 TTTTATTGAAAATTT
3936703 AAAGTTTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
28 2 0.05
29 13 0.31
30 1 0.02
31 7 0.17
32 9 0.21
33 10 0.24
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (31 bp):
TTTTATTGAAAATTTTTGTTTTTTATTAATT
Found at i:3936816 original size:10 final size:10
Alignment explanation
Indices: 3936803--3936827 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3936793 TTTATATATA
3936803 TTTTTAGAAT
1 TTTTTAGAAT
3936813 TTTTTAGAAT
1 TTTTTAGAAT
3936823 TTTTT
1 TTTTT
3936828 GAAAATTTCT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTAGAAT
Found at i:3937623 original size:22 final size:21
Alignment explanation
Indices: 3937597--3937752 Score: 77
Period size: 22 Copynumber: 7.2 Consensus size: 21
3937587 AATTAACCAG
3937597 TAATAACTTAATAGTAAATCA
1 TAATAACTTAATAGTAAATCA
** * *
3937618 TAAATAACTTTTTTA-TAAGTTA
1 T-AATAAC-TTAATAGTAAATCA
* *
3937640 GTGATAACTTAATAGTAAATGAA
1 -TAATAACTTAATAGTAAAT-CA
* * *
3937663 TGAA-AATTTAATAGTCAATAA
1 T-AATAACTTAATAGTAAATCA
*
3937684 TTTATAACTTAATAGTAAATCAA
1 -TAATAACTTAATAGTAAATC-A
* * *
3937707 TAACAACAT-ATAGTAATTGCA
1 TAATAACTTAATAGTAAAT-CA
* *
3937728 TAATAATTTAGTAGTAAATCA
1 TAATAACTTAATAGTAAATCA
3937749 -AATA
1 TAATA
3937753 TAATATAGTT
Statistics
Matches: 99, Mismatches: 25, Indels: 23
0.67 0.17 0.16
Matches are distributed among these distances:
20 4 0.04
21 25 0.25
22 62 0.63
23 8 0.08
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (21 bp):
TAATAACTTAATAGTAAATCA
Found at i:3938877 original size:23 final size:23
Alignment explanation
Indices: 3938851--3938894 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3938841 TTAAAAATAG
3938851 TTTAAATTAATAAAAATAATATT
1 TTTAAATTAATAAAAATAATATT
3938874 TTTAAATTAATAAAAATAATA
1 TTTAAATTAATAAAAATAATA
3938895 GCAATATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAATTAATAAAAATAATATT
Found at i:3939284 original size:22 final size:21
Alignment explanation
Indices: 3939270--3939320 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
3939260 TAAATCAAAG
3939270 ATAATTTTGTAGTAAATAATTA
1 ATAATTTTGTAGTAAATAA-TA
* *
3939292 ATAATTTTGTAGTTAATTATTA
1 ATAATTTTGTAG-TAAATAATA
3939314 ATAATTT
1 ATAATTT
3939321 AAAAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (21 bp):
ATAATTTTGTAGTAAATAATA
Found at i:3939370 original size:22 final size:22
Alignment explanation
Indices: 3939345--3939425 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 22
3939335 AGAGAATAGG
*
3939345 AAATCATTGATAATTTAATAAT
1 AAATCATTAATAATTTAATAAT
* * * *
3939367 AAATTATAAATAATTTAGTAGT
1 AAATCATTAATAATTTAATAAT
* * *
3939389 AAATCAATAATAATTTTATATT
1 AAATCATTAATAATTTAATAAT
* *
3939411 AAATAATTAAAAATT
1 AAATCATTAATAATT
3939426 AAGATAATCG
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
AAATCATTAATAATTTAATAAT
Found at i:3939495 original size:22 final size:22
Alignment explanation
Indices: 3939470--3939540 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
3939460 AACATAAGTT
*
3939470 TAAATGCA-TAATAATATAATAG
1 TAAAT-CATTAATAATATAATAA
* *
3939492 TAAATCATTGATAATTTAATAA
1 TAAATCATTAATAATATAATAA
* * *
3939514 TAAATTATTGATAATTTAATAA
1 TAAATCATTAATAATATAATAA
*
3939536 CAAAT
1 TAAAT
3939541 TGATAACTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 2 0.05
22 41 0.95
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATAATATAATAA
Found at i:3939535 original size:19 final size:19
Alignment explanation
Indices: 3939492--3939553 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
3939482 AATATAATAG
*
3939492 TAAATCATTGATAATTTAATAA
1 TAAATAATTGATAA-TT--TAA
*
3939514 TAAATTATTGATAATTTAA
1 TAAATAATTGATAATTTAA
*
3939533 TAACA-AATTGATAACTTAA
1 TAA-ATAATTGATAATTTAA
3939552 TA
1 TA
3939554 TTAAATCACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 20 0.56
20 1 0.03
21 2 0.06
22 13 0.36
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAATAATTGATAATTTAA
Found at i:3939541 original size:22 final size:22
Alignment explanation
Indices: 3939493--3939541 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3939483 ATATAATAGT
* *
3939493 AAATCATTGATAATTTAATAAT
1 AAATTATTGATAATTTAATAAC
3939515 AAATTATTGATAATTTAATAAC
1 AAATTATTGATAATTTAATAAC
3939537 AAATT
1 AAATT
3939542 GATAACTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (22 bp):
AAATTATTGATAATTTAATAAC
Found at i:3939656 original size:22 final size:22
Alignment explanation
Indices: 3939631--3939699 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
3939621 TAAATTAGTT
*
3939631 AATCAATGATAATTTTATAATA
1 AATCAATGATAAATTTATAATA
* *
3939653 AATCATTGATAAATTTATAGTA
1 AATCAATGATAAATTTATAATA
* * *
3939675 AATCCATTATAACTTTATAATA
1 AATCAATGATAAATTTATAATA
3939697 AAT
1 AAT
3939700 TATCAATAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
AATCAATGATAAATTTATAATA
Found at i:3939708 original size:22 final size:22
Alignment explanation
Indices: 3939639--3939711 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
3939629 TTAATCAATG
* **
3939639 ATAATTTTATAATAAATCATTG
1 ATAACTTTATAATAAATCATCA
* * *
3939661 ATAAATTTATAGTAAATCCAT-T
1 ATAACTTTATAATAAAT-CATCA
*
3939683 ATAACTTTATAATAAATTATCA
1 ATAACTTTATAATAAATCATCA
3939705 ATAACTT
1 ATAACTT
3939712 AGTAGTAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.05
22 37 0.88
23 3 0.07
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (22 bp):
ATAACTTTATAATAAATCATCA
Found at i:3939720 original size:22 final size:22
Alignment explanation
Indices: 3939651--3939868 Score: 134
Period size: 22 Copynumber: 9.9 Consensus size: 22
3939641 AATTTTATAA
* * * *
3939651 TAAATCATTGATAAATTTATAG
1 TAAATTATTAATAACTTAATAG
* * *
3939673 TAAATCCATT-ATAACTTTATAA
1 TAAAT-TATTAATAACTTAATAG
* *
3939695 TAAATTATCAATAACTTAGTAG
1 TAAATTATTAATAACTTAATAG
* * * *
3939717 TAAATTATCAACAATTTAATGG
1 TAAATTATTAATAACTTAATAG
* *
3939739 TAAATTATTTATAACTTAATGG
1 TAAATTATTAATAACTTAATAG
* * * *
3939761 TAAATCATTAATAAATTACTAA
1 TAAATTATTAATAACTTAATAG
* * * * *
3939783 TAAATCATTGACAATTTATTAG
1 TAAATTATTAATAACTTAATAG
* *
3939805 TAAATTATTAAAAAATTAATAG
1 TAAATTATTAATAACTTAATAG
* **
3939827 TAAATTACTAATAA-TATAGCAG
1 TAAATTATTAATAACT-TAATAG
*
3939849 TAAATTAATAATAACTTAAT
1 TAAATTATTAATAACTTAAT
3939869 TGTCTATCAT
Statistics
Matches: 154, Mismatches: 38, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
21 3 0.02
22 146 0.95
23 5 0.03
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (22 bp):
TAAATTATTAATAACTTAATAG
Found at i:3939765 original size:66 final size:65
Alignment explanation
Indices: 3939664--3939855 Score: 165
Period size: 66 Copynumber: 2.9 Consensus size: 65
3939654 ATCATTGATA
* * *
3939664 AATTT-ATAGTAAATCCA-TTATAACTTTATAATAAATTATCAATAACTTAGTAGTAAATTATCA
1 AATTTAATAGTAAAT-TATTTATAACTTAATAGTAAATTATCAATAA-TTAGTAGTAAATTATCA
3939727 AC
64 AC
* * * * * * * **
3939729 AATTTAATGGTAAATTATTTATAACTTAATGGTAAATCATTAATAAATTACTAATAAATCATTGA
1 AATTTAATAGTAAATTATTTATAACTTAATAGTAAATTATCAAT-AATTAGTAGTAAATTATCAA
3939794 C
65 C
* * * * *
3939795 AATTTATTAGTAAATTATTAAAAAATTAATAGTAAATTA-CTAATAATATAGCAGTAAATTA
1 AATTTAATAGTAAATTATTTATAACTTAATAGTAAATTATC-AATAAT-TAGTAGTAAATTA
3939856 ATAATAACTT
Statistics
Matches: 98, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
65 9 0.09
66 87 0.89
67 2 0.02
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (65 bp):
AATTTAATAGTAAATTATTTATAACTTAATAGTAAATTATCAATAATTAGTAGTAAATTATCAAC
Found at i:3939783 original size:11 final size:11
Alignment explanation
Indices: 3939692--3939840 Score: 64
Period size: 11 Copynumber: 13.5 Consensus size: 11
3939682 TATAACTTTA
3939692 TAATAAATTAT
1 TAATAAATTAT
* * *
3939703 CAATAACTTAG
1 TAATAAATTAT
*
3939714 TAGTAAATTAT
1 TAATAAATTAT
* * * *
3939725 CAACAATTTAA
1 TAATAAATTAT
**
3939736 TGGTAAATTAT
1 TAATAAATTAT
* * *
3939747 TTATAACTTAA
1 TAATAAATTAT
** *
3939758 TGGTAAATCAT
1 TAATAAATTAT
*
3939769 TAATAAATTAC
1 TAATAAATTAT
*
3939780 TAATAAATCAT
1 TAATAAATTAT
* * *
3939791 TGACAATTTAT
1 TAATAAATTAT
*
3939802 TAGTAAATTAT
1 TAATAAATTAT
* *
3939813 TAAAAAATTAA
1 TAATAAATTAT
* *
3939824 TAGTAAATTAC
1 TAATAAATTAT
3939835 TAATAA
1 TAATAA
3939841 TATAGCAGTA
Statistics
Matches: 90, Mismatches: 48, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
11 90 1.00
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (11 bp):
TAATAAATTAT
Found at i:3940364 original size:22 final size:21
Alignment explanation
Indices: 3940322--3940585 Score: 133
Period size: 22 Copynumber: 12.1 Consensus size: 21
3940312 TGAAAAATAA
*
3940322 AGTAAATTAAT-ATAACCTAAT
1 AGTAAATT-ATGATAACTTAAT
3940343 AGTAAATTATCGATAACTTAAT
1 AGTAAATTAT-GATAACTTAAT
* *
3940365 AGTTAATCAATGATAACTTAAT
1 AGTAAAT-TATGATAACTTAAT
* * *
3940387 AATAAATTATGAAAATTTTAAT
1 AGTAAATTATGATAA-CTTAAT
* * **
3940409 -GTAAATCAATGATAAATTGGT
1 AGTAAAT-TATGATAACTTAAT
* *
3940430 AGTGAATTATAGATAATTTAAT
1 AGTAAATTAT-GATAACTTAAT
* * *
3940452 A-TAAATATATGATGATTTTAT
1 AGTAAAT-TATGATAACTTAAT
* *
3940473 AGTAAATAATCGAAAAC-TAGAT
1 AGTAAATTAT-GATAACTTA-AT
* *
3940495 TGTAAATAAATGATAA-TATAAT
1 AGTAAAT-TATGATAACT-TAAT
* * *
3940517 AGTAAATGTATAATAACATATT
1 AGTAAAT-TATGATAACTTAAT
* * *
3940539 AGTAATTTATTGATAATTTAGT
1 AGTAAATTA-TGATAACTTAAT
*
3940561 AGTAAATTATTAATAACTTAAT
1 AGTAAATTA-TGATAACTTAAT
3940583 AGT
1 AGT
3940586 CATAAATCGG
Statistics
Matches: 183, Mismatches: 44, Indels: 31
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.01
21 43 0.23
22 131 0.72
23 7 0.04
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (21 bp):
AGTAAATTATGATAACTTAAT
Found at i:3940387 original size:44 final size:43
Alignment explanation
Indices: 3940322--3940585 Score: 162
Period size: 44 Copynumber: 6.1 Consensus size: 43
3940312 TGAAAAATAA
* *
3940322 AGTAAATTAAT-ATAACCTAATAGTAAATTATCGATAACTTAAT
1 AGTAAATCAATGATAACTTAATAGTAAATTAT-GATAACTTAAT
* * * *
3940365 AGTTAATCAATGATAACTTAATAATAAATTATGAAAATTTTAAT
1 AGTAAATCAATGATAACTTAATAGTAAATTATGATAA-CTTAAT
* ** * *
3940409 -GTAAATCAATGATAAATTGGTAGTGAATTATAGATAATTTAAT
1 AGTAAATCAATGATAACTTAATAGTAAATTAT-GATAACTTAAT
* * * * *
3940452 A-TAAAT-ATATGATGATTTTATAGTAAATAATCGAAAAC-TAGAT
1 AGTAAATCA-ATGATAACTTAATAGTAAATTAT-GATAACTTA-AT
* * * * *
3940495 TGTAAATAAATGATAA-TATAATAGTAAATGTATAATAACATATT
1 AGTAAATCAATGATAACT-TAATAGTAAAT-TATGATAACTTAAT
* * * * * *
3940539 AGTAATTTATTGATAATTTAGTAGTAAATTATTAATAACTTAAT
1 AGTAAATCAATGATAACTTAATAGTAAATTA-TGATAACTTAAT
3940583 AGT
1 AGT
3940586 CATAAATCGG
Statistics
Matches: 172, Mismatches: 36, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
42 3 0.02
43 75 0.44
44 88 0.51
45 6 0.03
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (43 bp):
AGTAAATCAATGATAACTTAATAGTAAATTATGATAACTTAAT
Found at i:3940620 original size:22 final size:22
Alignment explanation
Indices: 3940551--3940620 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
3940541 TAATTTATTG
*
3940551 ATAATTTAGTAGTAAATTA-TT
1 ATAATTTAGTAATAAATTAGTT
* **
3940572 AATAACTTAATAGTCATAAATCGGTT
1 -ATAA-TT--TAGTAATAAATTAGTT
3940598 ATAATTTAGTAATAAATTAGTT
1 ATAATTTAGTAATAAATTAGTT
3940620 A
1 A
3940621 ATCATTAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
22 18 0.49
23 2 0.05
24 2 0.05
25 13 0.35
26 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (22 bp):
ATAATTTAGTAATAAATTAGTT
Found at i:3940720 original size:22 final size:22
Alignment explanation
Indices: 3940640--3940720 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
3940630 AATTTTGAAT
* * *
3940640 TAAATCATCGATAAATTAATAG
1 TAAATCATTGATAACTTAATAA
* *
3940662 TAAATAAATT-ATAACTTTATAA
1 TAAAT-CATTGATAACTTAATAA
* *
3940684 TAAAT-AATCATTAACTTAATAA
1 TAAATCATTGA-TAACTTAATAA
3940706 TAAATCATTGATAAC
1 TAAATCATTGATAAC
3940721 ATATTATTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 38 0.83
23 5 0.11
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAATCATTGATAACTTAATAA
Found at i:3940891 original size:13 final size:13
Alignment explanation
Indices: 3940870--3940900 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3940860 TATGAACTTA
3940870 TTTAATAAAAAAT
1 TTTAATAAAAAAT
*
3940883 TTTATTAAAAAAT
1 TTTAATAAAAAAT
3940896 TTTAA
1 TTTAA
3940901 ATTTGAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTAATAAAAAAT
Found at i:3941039 original size:20 final size:22
Alignment explanation
Indices: 3941011--3941054 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3941001 ATACAAATTT
3941011 TATCAAT-AATTACCAAAAATA
1 TATCAATAAATTACCAAAAATA
* *
3941032 TATC-ATAAATTGCCAAAATTA
1 TATCAATAAATTACCAAAAATA
3941053 TA
1 TA
3941055 AGAAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (22 bp):
TATCAATAAATTACCAAAAATA
Found at i:3941181 original size:21 final size:21
Alignment explanation
Indices: 3941157--3941197 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3941147 ATCAAACTAA
*
3941157 TATTGAATATTATTAAAATTG
1 TATTGAAAATTATTAAAATTG
3941178 TATTGAAAATTATTAAAATT
1 TATTGAAAATTATTAAAATT
3941198 TTATCAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
TATTGAAAATTATTAAAATTG
Found at i:3941773 original size:50 final size:49
Alignment explanation
Indices: 3941663--3941780 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 49
3941653 GTTTTGTTCA
* *
3941663 AGAATTATTTTTTATAAAAAAATATTTTATTTGTTAAATCTATAAAGTG
1 AGAATTATTTTTTATAAAAAAATACTTTATTTGTTAAATATATAAAGTG
* * * * * * *
3941712 GGAATTATTTTTTTTATAAAAATACTTTGTTTGTTTACTATGTAAAGTG
1 AGAATTATTTTTTATAAAAAAATACTTTATTTGTTAAATATATAAAGTG
* *
3941761 AGAATTACTTTTTATTAAAA
1 AGAATTATTTTTTATAAAAA
3941781 GTATTTTGTT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (49 bp):
AGAATTATTTTTTATAAAAAAATACTTTATTTGTTAAATATATAAAGTG
Found at i:3947159 original size:20 final size:20
Alignment explanation
Indices: 3947134--3947172 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3947124 AATTTTTATA
3947134 TATCTATTTATCTATATATC
1 TATCTATTTATCTATATATC
* *
3947154 TATCTATTTGTTTATATAT
1 TATCTATTTATCTATATAT
3947173 ATAAAATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (20 bp):
TATCTATTTATCTATATATC
Found at i:3949073 original size:27 final size:26
Alignment explanation
Indices: 3949043--3949232 Score: 79
Period size: 26 Copynumber: 7.2 Consensus size: 26
3949033 AACTAATTTC
*
3949043 AAATTAAAAAATATGAAAATTTCTTAA
1 AAATTAAAAAATATAAAAATTT-TTAA
* * * *
3949070 AAATCATAAAATTTTAATAA-TTTTAA
1 AAATTA-AAAAATATAAAAATTTTTAA
* *
3949096 AAATTCAAAAAAAATTAAAAATTTGATAA
1 AAATT-AAAAAATA-TAAAAATTT-TTAA
* *
3949125 AAATCTAAAAAAT-TCAAGAAA--ATGAA
1 AAAT-TAAAAAATAT-AA-AAATTTTTAA
*
3949151 AATTTTAATAAAA-A-AAAAATTATTTAA
1 AA-ATTAA-AAAATATAAAAATT-TTTAA
* * * *
3949178 AATTTAAAAAATTTTAAAATTTTAAA
1 AAATTAAAAAATATAAAAATTTTTAA
* * *
3949204 AAACT-AAAAATAAAAAAATTTTTGA
1 AAATTAAAAAATATAAAAATTTTTAA
3949229 AAAT
1 AAAT
3949233 ATTTGAAAAA
Statistics
Matches: 118, Mismatches: 29, Indels: 34
0.65 0.16 0.19
Matches are distributed among these distances:
24 3 0.03
25 24 0.20
26 31 0.26
27 30 0.25
28 13 0.11
29 16 0.14
30 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (26 bp):
AAATTAAAAAATATAAAAATTTTTAA
Found at i:3949106 original size:54 final size:53
Alignment explanation
Indices: 3949004--3949134 Score: 124
Period size: 54 Copynumber: 2.4 Consensus size: 53
3948994 AAGATTTCAT
* * * * *
3949004 AAAATTTTTTAAAAAATACAAAAAATTATAACTAATTTCAAATTAAAAAATA-TG
1 AAAATTTCTT-AAAAAT-CATAAAATTATAACTAATTTAAAATTAAAAAAAATTA
*
3949058 AAAATTTCTTAAAAATCATAAAATTTTAA-TAATTTTAAAAATTCAAAAAAAATTA
1 AAAATTTCTTAAAAATCATAAAATTATAACTAA-TTT-AAAATT-AAAAAAAATTA
**
3949113 AAAATTTGATAAAAATC-TAAAA
1 AAAATTTCTTAAAAATCATAAAA
3949135 AATTCAAGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 3 0.05
52 14 0.22
53 11 0.17
54 21 0.32
55 16 0.25
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (53 bp):
AAAATTTCTTAAAAATCATAAAATTATAACTAATTTAAAATTAAAAAAAATTA
Found at i:3949109 original size:37 final size:34
Alignment explanation
Indices: 3949068--3949161 Score: 89
Period size: 38 Copynumber: 2.6 Consensus size: 34
3949058 AAAATTTCTT
* *
3949068 AAAAATCATAAAATTTTAATAATTTTAAAAATTCAAA
1 AAAAAT-A-AAAATTTTAATAATCTAAAAAATTC-AA
*
3949105 AAAAATTAAAAATTTGATAAAAATCTAAAAAATTCAA
1 AAAAA-TAAAAATTT--TAATAATCTAAAAAATTCAA
* *
3949142 GAAAATGAAAATTTTAATAA
1 AAAAATAAAAATTTTAATAA
3949162 AAAAAAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
34 5 0.10
36 15 0.31
37 12 0.25
38 16 0.33
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (34 bp):
AAAAATAAAAATTTTAATAATCTAAAAAATTCAA
Found at i:3949113 original size:18 final size:18
Alignment explanation
Indices: 3949092--3949146 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3949082 TTTAATAATT
3949092 TTAAAAATTCAAAAAAAA
1 TTAAAAATTCAAAAAAAA
** *
3949110 TTAAAAATTTGATAAAAA
1 TTAAAAATTCAAAAAAAA
3949128 TCTAAAAAATTCAAGAAAA
1 T-T-AAAAATTCAA-AAAA
3949147 TGAAAATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 16 0.57
19 1 0.04
20 8 0.29
21 3 0.11
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.25
Consensus pattern (18 bp):
TTAAAAATTCAAAAAAAA
Found at i:3949186 original size:17 final size:18
Alignment explanation
Indices: 3949173--3949206 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3949163 AAAAAAATTA
3949173 TTTAAAA-TTTAAAAAAT
1 TTTAAAATTTTAAAAAAT
3949190 TTTAAAATTTTAAAAAA
1 TTTAAAATTTTAAAAAA
3949207 CTAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAAAATTTTAAAAAAT
Found at i:3949577 original size:10 final size:10
Alignment explanation
Indices: 3949564--3949588 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3949554 TTTATATATA
3949564 TTTTTAGAAT
1 TTTTTAGAAT
3949574 TTTTTAGAAT
1 TTTTTAGAAT
3949584 TTTTT
1 TTTTT
3949589 GAAAATTTCT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTAGAAT
Found at i:3950291 original size:22 final size:21
Alignment explanation
Indices: 3950266--3950362 Score: 74
Period size: 22 Copynumber: 4.6 Consensus size: 21
3950256 ATAGTAGATA
3950266 ATTGATAACTTATTAATTAATC
1 ATTGATAACTTA-TAATTAATC
* *
3950288 ATTGAAAAACTTA-AAATAATC
1 ATTG-ATAACTTATAATTAATC
* *
3950309 AGT-ATAACTTAGT-AGTAATC
1 ATTGATAACTTA-TAATTAATC
*
3950329 ATTGATAACTTAAAAATTAATC
1 ATTGATAACTT-ATAATTAATC
* *
3950351 ACTAATAACTTA
1 ATTGATAACTTA
3950363 ATAGTAAATC
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
19 7 0.12
20 8 0.14
21 17 0.29
22 20 0.34
23 7 0.12
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (21 bp):
ATTGATAACTTATAATTAATC
Found at i:3950331 original size:41 final size:44
Alignment explanation
Indices: 3950283--3950383 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 44
3950273 ACTTATTAAT
* * *
3950283 TAATCATTGAAAAACTT-AAAA-TAATCAGT-ATAACTTAGTAG
1 TAATCATTGAATAACTTAAAAATTAATCACTAATAACTTAATAG
3950324 TAATCATTG-ATAACTTAAAAATTAATCACTAATAACTTAATAG
1 TAATCATTGAATAACTTAAAAATTAATCACTAATAACTTAATAG
3950367 TAAATCA-TGAATAACTT
1 T-AATCATTGAATAACTT
3950384 TGTTGTAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
40 6 0.12
41 13 0.25
42 7 0.13
43 14 0.27
44 12 0.23
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.34
Consensus pattern (44 bp):
TAATCATTGAATAACTTAAAAATTAATCACTAATAACTTAATAG
Found at i:3950347 original size:63 final size:65
Alignment explanation
Indices: 3950257--3950408 Score: 159
Period size: 65 Copynumber: 2.4 Consensus size: 65
3950247 AATAATATAA
** * *
3950257 TAGTAGATAATTGATAACTTATTAATTAATCATTGAAAAACTTAA-AAT-AATCA-GTATAACTT
1 TAGTA-ATAATTGATAACTTAAAAATTAATCACT-AAAAACTTAATAATAAATCATGAATAACTT
3950319 AG
64 AG
* * * *
3950321 TAGTAATCATTGATAACTTAAAAATTAATCACTAATAACTTAATAGTAAATCATGAATAACTTTG
1 TAGTAATAATTGATAACTTAAAAATTAATCACTAAAAACTTAATAATAAATCATGAATAACTTAG
* *
3950386 TTGTAA-ATTATGATAACTTAAAA
1 TAGTAATAAT-TGATAACTTAAAA
3950409 GTAAATGAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
62 9 0.12
63 26 0.36
64 11 0.15
65 27 0.37
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (65 bp):
TAGTAATAATTGATAACTTAAAAATTAATCACTAAAAACTTAATAATAAATCATGAATAACTTAG
Found at i:3950372 original size:22 final size:21
Alignment explanation
Indices: 3950312--3950414 Score: 73
Period size: 22 Copynumber: 4.8 Consensus size: 21
3950302 AATAATCAGT
* *
3950312 ATAACTTAGTAGT-AATCATTG
1 ATAACTTAATAGTAAATCA-TA
* * *
3950333 ATAACTTAAAAATTAATCACTA
1 ATAACTTAATAGTAAATCA-TA
3950355 ATAACTTAATAGTAAATCATGA
1 ATAACTTAATAGTAAATCAT-A
** * * *
3950377 ATAACTTTGTTGTAAATTATG
1 ATAACTTAATAGTAAATCATA
*
3950398 ATAACTTAAAAGTAAAT
1 ATAACTTAATAGTAAAT
3950415 GAATGATAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
21 24 0.38
22 39 0.62
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
ATAACTTAATAGTAAATCATA
Done.