Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397279.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.0, 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: 2022356
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6073 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:585348 original size:16 final size:16
Alignment explanation
Indices: 585327--585357 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
585317 TGTCCCACGT
585327 TTTATTTATTTATTTG
1 TTTATTTATTTATTTG
585343 TTTATTTATTTATTT
1 TTTATTTATTTATTT
585358 TTGATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTATTTATTTATTTG
Found at i:599502 original size:4 final size:4
Alignment explanation
Indices: 599471--599539 Score: 51
Period size: 4 Copynumber: 18.0 Consensus size: 4
599461 AAAGATTTAT
* *
599471 AATA TATA AGTA AATA GAAT- AA-A AATA AATA AATA AATA AAT- -ATA
1 AATA AATA AATA AATA -AATA AATA AATA AATA AATA AATA AATA AATA
599516 AAT- AATA ATATA AATTA AA-A AATA
1 AATA AATA A-ATA AA-TA AATA AATA
599540 TAAAAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
2 2 0.04
3 10 0.19
4 29 0.56
5 11 0.21
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:599507 original size:14 final size:14
Alignment explanation
Indices: 599481--599548 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
599471 AATATATAAG
599481 TAAATAGAATAAAAA
1 TAAATA-AATAAAAA
599496 TAAATAAATAAATAA
1 TAAATAAATAAA-AA
*
599511 -ATATAAATAATAATA
1 TAAATAAATAA-AA-A
*
599526 TAAATTAAA-AAATA
1 TAAA-TAAATAAAAA
*
599540 TAAAAAAAT
1 TAAATAAAT
599549 TTTAAAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
13 3 0.07
14 21 0.49
15 11 0.26
16 4 0.09
17 4 0.09
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (14 bp):
TAAATAAATAAAAA
Found at i:599511 original size:18 final size:18
Alignment explanation
Indices: 599476--599529 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
599466 TTTATAATAT
*
599476 ATAAGTAAATAGAATAAAA
1 ATAAATAAATA-AATAAAA
*
599495 ATAAATAAATAAATAAAT
1 ATAAATAAATAAATAAAA
599513 ATAAAT-AATAATATAAA
1 ATAAATAAATAA-ATAAA
599530 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 5 0.16
18 17 0.53
19 10 0.31
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (18 bp):
ATAAATAAATAAATAAAA
Found at i:599530 original size:18 final size:17
Alignment explanation
Indices: 599469--599539 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
599459 CTAAAGATTT
*
599469 ATAATATATAAGTAAATAGA
1 ATAA-ATATAAAT-AATA-A
*
599489 ATAAAAATAAATAAATAA
1 ATAAATATAAAT-AATAA
599507 ATAAATATAAATAATAA
1 ATAAATATAAATAATAA
*
599524 TATAAAT-TAAAAAATA
1 -ATAAATATAAATAATA
599540 TAAAAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
17 13 0.28
18 18 0.39
19 11 0.24
20 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
ATAAATATAAATAATAA
Found at i:602858 original size:2 final size:2
Alignment explanation
Indices: 602851--602882 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
602841 TGATCCTAAT
*
602851 TA TA TA TA AA 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
602883 AAATTGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:603827 original size:21 final size:21
Alignment explanation
Indices: 603763--603829 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
603753 TATTAATAAA
*
603763 AAAATTATACATTGACAGAAT
1 AAAATTATACAATGACAGAAT
*
603784 AAAATCATATAAAAT-A-A-AAT
1 AAAAT--TATACAATGACAGAAT
603804 AAAATTATACAATGACAGAAT
1 AAAATTATACAATGACAGAAT
603825 AAAAT
1 AAAAT
603830 CATATAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
18 7 0.18
19 1 0.03
20 9 0.24
21 14 0.37
22 1 0.03
23 6 0.16
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.25
Consensus pattern (21 bp):
AAAATTATACAATGACAGAAT
Found at i:612018 original size:30 final size:29
Alignment explanation
Indices: 611937--612023 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
611927 TCAGAAAAAA
* * *
611937 TCAAATAAGTCTTTGTATTTTTATTGTGT
1 TCAAATAAGTCTTTATATTTTTATTTTGG
* * *
611966 TCAATTAAATCCTTATATTTTTTATTTTGAG
1 TCAAATAAGTCTTTATA-TTTTTATTTTG-G
*
611997 TCAAATAAGTTTTTATATTTTTATTTT
1 TCAAATAAGTCTTTATATTTTTATTTT
612024 AAGCTAAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 13 0.28
30 20 0.43
31 13 0.28
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (29 bp):
TCAAATAAGTCTTTATATTTTTATTTTGG
Found at i:624706 original size:2 final size:2
Alignment explanation
Indices: 624699--624728 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
624689 AGCTTTTCCA
*
624699 CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
624729 TTCCCAATGT
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:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:632216 original size:15 final size:15
Alignment explanation
Indices: 632196--632225 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
632186 TCTTAGAAAG
632196 GAAAAGAAAAAAGGA
1 GAAAAGAAAAAAGGA
*
632211 GAAAAGGAAAAAGGA
1 GAAAAGAAAAAAGGA
632226 AACTAACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
GAAAAGAAAAAAGGA
Found at i:638558 original size:3 final size:3
Alignment explanation
Indices: 638550--638580 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
638540 GTTCTATATC
638550 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
638581 CATTTGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:652370 original size:2 final size:2
Alignment explanation
Indices: 652363--652387 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
652353 AAAATATGAT
652363 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
652388 CCCAAGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:652833 original size:12 final size:12
Alignment explanation
Indices: 652818--652866 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
652808 AAAGTTTTAA
652818 TTATATATATAT
1 TTATATATATAT
* *
652830 TTATTTATAAAT
1 TTATATATATAT
652842 TTA-ATAT-TAT
1 TTATATATATAT
*
652852 TAATATA-ATAT
1 TTATATATATAT
652863 TTAT
1 TTAT
652867 TAAAATTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
10 4 0.14
11 12 0.41
12 13 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATATATATAT
Found at i:652866 original size:15 final size:15
Alignment explanation
Indices: 652831--652869 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
652821 TATATATATT
* *
652831 TATTTATAAATTTAA
1 TATTTATTAATATAA
652846 TA-TTATTAATATAA
1 TATTTATTAATATAA
652860 TATTTATTAA
1 TATTTATTAA
652870 AATTCATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTTATTAATATAA
Found at i:653320 original size:22 final size:22
Alignment explanation
Indices: 653278--653320 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
653268 TTACTTTTTA
**
653278 TATATTAAAAAGTATTGAAATC
1 TATATTAAAAAAAATTGAAATC
653300 TATATTATAAAAAAATT-AAAT
1 TATATTA-AAAAAAATTGAAAT
653321 TTTAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
TATATTAAAAAAAATTGAAATC
Found at i:669040 original size:117 final size:117
Alignment explanation
Indices: 668885--669610 Score: 443
Period size: 117 Copynumber: 6.2 Consensus size: 117
668875 TAAATTCAAG
* * * * *
668885 AAATATTTAAAATAA-TAATGCTTTTATTAAACTAATTAAATAATTTAACCACTTGAATTGAAAA
1 AAATATTTAAATTAATTAA-GGTTTCATTAAATTAATTAAATAATTTAACTACTTGAATTGAAAA
* * *
668949 AATGTTTTTGTTATTAAGCAATTAATTAAATTAGTAATATTATTTAATTTTTA
65 AATGTTTTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAATTTTTA
* *
669002 AAATATTTAAATTAATTAAGGTTTCATTAAATTAATTAAACAATTTGACTACTTGAATTGAAAAA
1 AAATATTTAAATTAATTAAGGTTTCATTAAATTAATTAAATAATTTAACTACTTGAATTG-AAAA
* * * * **
669067 AATGTTTTAGTTATTAAGCAATTAATTAAATTATTAATATTATTTAACTTAAA
65 AATGTTTTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAATTTTTA
* * * ** *
669120 AAATATTTAAATTAATTATTAAGG-TGCTAGTTATGAGTTAAATAAATAATTTAGTTAATTTAGT
1 AAATATTTAAATT-A--ATTAAGGTTTC-A-TTA--AATTAATTAAATAATTTAACT-ACTT-G-
* ** * * * *
669184 AA-TG-TAATGTGTTATAAGTAATTAAGCAATTAATTAAATTAATAATATTATATAATATTTC
56 AATTGAAAAAATGTT-TTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAATTTTTA
** * * * * *** * ** * ** * *
669245 ATTTATTTTAAGTAATTAAGGTATGAGGGAATTAGTTACGTAATTTAACTAATT-AAAAGGAATA
1 AAATATTTAAATTAATTAAGGTTTCATTAAATTAATTAAATAATTTAACTACTTGAATTGAAAAA
* * ** * * *
669309 ATGTATTAGCAATTAATAAATTAATTAAATTAATAATAGTATATAATATGTTA
66 ATGTTTTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAAT-TTTTA
*** * * * ** * * * ** *
669362 GGGTTTTTAAATTAATTAAGATTTAATGGAATTAATTACATAATTAAACTAAC-TAAAAAG-AAT
1 AAATATTTAAATTAATTAAGGTTTCATTAAATTAATTAAATAATTTAACT-ACTTGAATTGAAAA
* * * *
669425 TACGTATTAGTAATTAAGCAATTAATTAAATTAGTAA-ATTTAGTAAAATTATTT-
65 AATGTTTTAGTAATTAAGCAATTAATTAAATTAGTAATA-TTA-TATAATT-TTTA
* * * * *
669479 CATTATTTAAA-TAATTAAGGTTTCATTAAATTAATTAGATAATTTGACTACTTGAATTTAAAAA
1 AAATATTTAAATTAATTAAGGTTTCATTAAATTAATTAAATAATTTAACTACTTGAATTGAAAAA
* * * * * *
669543 ATG-TTTATTTATCAGGTAATTAATTAAATTAGTAATATTATTTAA--TTTA
66 ATGTTTTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAATTTTTA
*
669592 AAGTTATTTAAATTAATTA
1 AA-ATATTTAAATTAATTA
669611 TTAAGGTTCA
Statistics
Matches: 467, Mismatches: 114, Indels: 58
0.73 0.18 0.09
Matches are distributed among these distances:
112 3 0.01
113 1 0.00
114 9 0.02
115 13 0.03
116 102 0.22
117 142 0.30
118 84 0.18
119 15 0.03
120 2 0.00
121 8 0.02
122 11 0.02
124 22 0.05
125 50 0.11
126 3 0.01
127 2 0.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (117 bp):
AAATATTTAAATTAATTAAGGTTTCATTAAATTAATTAAATAATTTAACTACTTGAATTGAAAAA
ATGTTTTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAATTTTTA
Found at i:669110 original size:118 final size:118
Alignment explanation
Indices: 668885--669137 Score: 375
Period size: 118 Copynumber: 2.2 Consensus size: 118
668875 TAAATTCAAG
* * *
668885 AAATATTTAAAATAA-TAATGCTTTTATTAAACTAATTAAATAATTTAACCACTTGAATTGAAAA
1 AAATATTTAAATTAATTAATGCTTTCATTAAACTAATTAAACAATTTAACCACTTGAATTGAAAA
* * **
668949 AATGTTTTTGTTATTAAGCAATTAATTAAATTAGTAATATTATTTAATTTTTA
66 AATGTTTTAGTTATTAAGCAATTAATTAAATTAGTAATATTATTTAACTTAAA
* * * *
669002 AAATATTTAAATTAATTAA-GGTTTCATTAAATTAATTAAACAATTTGACTACTTGAATTGAAAA
1 AAATATTTAAATTAATTAATGCTTTCATTAAACTAATTAAACAATTTAACCACTTGAATTG-AAA
*
669066 AAATGTTTTAGTTATTAAGCAATTAATTAAATTATTAATATTATTTAACTTAAA
65 AAATGTTTTAGTTATTAAGCAATTAATTAAATTAGTAATATTATTTAACTTAAA
669120 AAATATTTAAATTAATTA
1 AAATATTTAAATTAATTA
669138 TTAAGGTGCT
Statistics
Matches: 122, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
117 49 0.40
118 73 0.60
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (118 bp):
AAATATTTAAATTAATTAATGCTTTCATTAAACTAATTAAACAATTTAACCACTTGAATTGAAAA
AATGTTTTAGTTATTAAGCAATTAATTAAATTAGTAATATTATTTAACTTAAA
Found at i:672825 original size:21 final size:21
Alignment explanation
Indices: 672773--672825 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
672763 AGAATCAAAG
* * *
672773 GAAGAAAACGAAAATGATATC
1 GAAGAAAATGAAAATGAGAAC
* **
672794 GATGACGATGAAAATGAGAAC
1 GAAGAAAATGAAAATGAGAAC
672815 GAAGAAAATGA
1 GAAGAAAATGA
672826 GTTCATTTTT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.08, G:0.25, T:0.13
Consensus pattern (21 bp):
GAAGAAAATGAAAATGAGAAC
Found at i:674258 original size:2 final size:2
Alignment explanation
Indices: 674251--674277 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
674241 TACATGTGTT
674251 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
674278 GTATGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:674290 original size:12 final size:12
Alignment explanation
Indices: 674275--674299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
674265 TATATATATA
674275 TATGTATGTGTG
1 TATGTATGTGTG
674287 TATGTATGTGTG
1 TATGTATGTGTG
674299 T
1 T
674300 GTGTGTGTTG
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:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (12 bp):
TATGTATGTGTG
Found at i:675706 original size:25 final size:25
Alignment explanation
Indices: 675669--675731 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
675659 AATAGAGAAG
* * * *
675669 AAGAAGGAAAAATCGATTTTGAAAA
1 AAGAAAGAGAAATCCATTTAGAAAA
675694 AAGAAAGAGAAATCCATTTAGAAAA
1 AAGAAAGAGAAATCCATTTAGAAAA
675719 ACA-AAAGAGAAAT
1 A-AGAAAGAGAAAT
675732 TGACTTCGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.16
Consensus pattern (25 bp):
AAGAAAGAGAAATCCATTTAGAAAA
Found at i:678797 original size:35 final size:33
Alignment explanation
Indices: 678723--678796 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 33
678713 TTTTAATGTC
*
678723 ATATATTTTATTTTCAATTTTCATTATAATCTT
1 ATATATTTTATTTTCAATTTTCAATATAATCTT
* *
678756 ATATATTTTATTTTTCATTTCTTTAATATAATTTCTT
1 ATATATTTTA-TTTTCAATT-TTCAATATAA--TCTT
678793 ATAT
1 ATAT
678797 TATATATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 10 0.29
34 8 0.24
35 8 0.24
37 8 0.24
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (33 bp):
ATATATTTTATTTTCAATTTTCAATATAATCTT
Found at i:678872 original size:56 final size:55
Alignment explanation
Indices: 678785--678925 Score: 167
Period size: 56 Copynumber: 2.5 Consensus size: 55
678775 TCTTTAATAT
*
678785 AATTTCTTATATTATATATTTATTTAATTTCTTGTACCTAAATTATATAAATTTTG
1 AATTTCTTATATTTTAT-TTTATTTAATTTCTTGTACCTAAATTATATAAATTTTG
** * * ** *
678841 AATTTCTTATATTTTATTTTATTTTCTTTTCTTTTACCTATATTATATATCTTTTT
1 AATTTCTTATATTTTATTTTA-TTTAATTTCTTGTACCTAAATTATATAAATTTTG
*
678897 AATTTCTTATA-TTTATTTTCTTATAATTT
1 AATTTCTTATATTTTATTTTATT-TAATTT
678926 TTATTTCTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
54 2 0.03
55 16 0.22
56 54 0.75
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (55 bp):
AATTTCTTATATTTTATTTTATTTAATTTCTTGTACCTAAATTATATAAATTTTG
Found at i:678903 original size:31 final size:30
Alignment explanation
Indices: 678792--678907 Score: 98
Period size: 31 Copynumber: 3.9 Consensus size: 30
678782 TATAATTTCT
*
678792 TATATTATATATTTATTTAATTTCTTGTACC
1 TATATTATATATTT-TTTAATTTCTTATACC
* * * *
678823 TAAATTATATAAATTTTGAATTTCTTATA-T
1 TATATTATAT-ATTTTTTAATTTCTTATACC
* * *
678853 TTTATT-T-TATTTTCT--TTTCTTTTACC
1 TATATTATATATTTTTTAATTTCTTATACC
678879 TATATTATATATCTTTTTAATTTCTTATA
1 TATATTATATAT-TTTTTAATTTCTTATA
678908 TTTATTTTCT
Statistics
Matches: 63, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
25 8 0.13
26 5 0.08
27 5 0.08
28 4 0.06
29 5 0.08
30 4 0.06
31 29 0.46
32 3 0.05
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (30 bp):
TATATTATATATTTTTTAATTTCTTATACC
Found at i:678916 original size:14 final size:14
Alignment explanation
Indices: 678894--678968 Score: 57
Period size: 14 Copynumber: 5.3 Consensus size: 14
678884 TATATATCTT
*
678894 TTTAATTTCTTATA
1 TTTATTTTCTTATA
678908 TTTATTTTCTTATAA
1 TTTATTTTCTTAT-A
*
678923 TTTTTATTTCTTATA
1 TTTAT-TTTCTTATA
*
678938 TTATATATT-TTAT-
1 TT-TATTTTCTTATA
*
678951 TTTAATTTTTTTAT-
1 TTT-ATTTTCTTATA
678965 TTTA
1 TTTA
678969 ATTATAACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
12 1 0.02
13 7 0.14
14 23 0.45
15 10 0.20
16 10 0.20
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTTCTTATA
Found at i:678946 original size:16 final size:15
Alignment explanation
Indices: 678894--678947 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
678884 TATATATCTT
678894 TTTA-ATTTCTTATA
1 TTTATATTTCTTATA
678908 TTTAT-TTTCTTATAA
1 TTTATATTTCTTAT-A
*
678923 TTTTTATTTCTTATA
1 TTTATATTTCTTATA
678938 TTATATATTT
1 TT-TATATTT
678948 TATTTTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.35
15 8 0.24
16 14 0.41
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATTTCTTATA
Found at i:678969 original size:14 final size:14
Alignment explanation
Indices: 678945--678971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
678935 ATATTATATA
678945 TTTTATTTTAATTT
1 TTTTATTTTAATTT
678959 TTTTATTTTAATT
1 TTTTATTTTAATT
678972 ATAACATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTAATTT
Found at i:680865 original size:14 final size:16
Alignment explanation
Indices: 680846--680877 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
680836 CAACAATGTG
680846 TTCCTTT-TATT-ATT
1 TTCCTTTCTATTAATT
680860 TTCCTTTCTATTAATT
1 TTCCTTTCTATTAATT
680876 TT
1 TT
680878 TATTCTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCCTTTCTATTAATT
Found at i:691166 original size:2 final size:2
Alignment explanation
Indices: 691159--691196 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
691149 CCTAAAGCTC
*
691159 TA TA TA TA TT 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
691197 AAAATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:703919 original size:14 final size:14
Alignment explanation
Indices: 703900--703927 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
703890 GCCCCAAACG
703900 ATTCTAATTAACAT
1 ATTCTAATTAACAT
703914 ATTCTAATTAACAT
1 ATTCTAATTAACAT
703928 GTATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTCTAATTAACAT
Found at i:704308 original size:58 final size:58
Alignment explanation
Indices: 704238--704347 Score: 202
Period size: 58 Copynumber: 1.9 Consensus size: 58
704228 CTTATGGCAT
*
704238 GTGAGTCCCAATAATTGCTTAGCTCAATCATGAAAGAGTCATTAAATTAATTCCATAA
1 GTGAGTCCCAATAATTGCTTAGCTCAATCATGAAAGAGTAATTAAATTAATTCCATAA
*
704296 GTGAGTCCCAATAATTGCTTAGGTCAATCATGAAAGAGTAATTAAATTAATT
1 GTGAGTCCCAATAATTGCTTAGCTCAATCATGAAAGAGTAATTAAATTAATT
704348 TATTTTCCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (58 bp):
GTGAGTCCCAATAATTGCTTAGCTCAATCATGAAAGAGTAATTAAATTAATTCCATAA
Found at i:705316 original size:2 final size:2
Alignment explanation
Indices: 705309--705341 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
705299 CTCAATTGAT
705309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
705342 TGGAGGATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:707417 original size:5 final size:5
Alignment explanation
Indices: 707407--707439 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
707397 CTCATTTCGC
*
707407 TTCCT TTCCT TTCCT TTCCT TTCCT TTCGT TTC
1 TTCCT TTCCT TTCCT TTCCT TTCCT TTCCT TTC
707440 AATTCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (5 bp):
TTCCT
Found at i:714103 original size:30 final size:28
Alignment explanation
Indices: 714063--714138 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
714053 AAATATTAAT
* **
714063 AATAAGAATTTATTTGATTTAAAATAAAA
1 AATAAAAATTTATTT-AAATAAAATAAAA
* *
714092 ATATAAAAATTTAATTAAATATAATAAAA
1 A-ATAAAAATTTATTTAAATAAAATAAAA
*
714121 AATAAAAATATATTTAAA
1 AATAAAAATTTATTTAAA
714139 ATTTTTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 15 0.38
29 12 0.31
30 12 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAAAAATTTATTTAAATAAAATAAAA
Found at i:714149 original size:20 final size:21
Alignment explanation
Indices: 714126--714173 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
714116 TAAAAAATAA
714126 AAATATATTTAAAAT-TTTTT
1 AAATATATTTAAAATATTTTT
714146 AAATA-ATTTAAAATATTTTT
1 AAATATATTTAAAATATTTTT
714166 AAA-ATATT
1 AAATATATT
714174 ATACTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATATTTAAAATATTTTT
Found at i:714159 original size:36 final size:35
Alignment explanation
Indices: 714079--714160 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
714069 AATTTATTTG
714079 ATTTAAAATAAAAATATAAAAATTTAATTAAATATA
1 ATTTAAAATAAAAATATAAAAATTT-ATTAAATATA
** *
714115 ATAAAAAATAAAAATATATTTAAAATTT-TTTAA-ATA
1 ATTTAAAATAAAAATATA---AAAATTTATTAAATATA
714151 ATTTAAAATA
1 ATTTAAAATA
714161 TTTTTAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
36 27 0.71
37 4 0.11
39 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (35 bp):
ATTTAAAATAAAAATATAAAAATTTATTAAATATA
Found at i:714168 original size:11 final size:11
Alignment explanation
Indices: 714125--714173 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
714115 ATAAAAAATA
*
714125 AAAATATATTT
1 AAAATATTTTT
714136 AAAAT-TTTTT
1 AAAATATTTTT
*
714146 -AAATA-ATTT
1 AAAATATTTTT
714155 AAAATATTTTT
1 AAAATATTTTT
714166 AAAATATT
1 AAAATATT
714174 ATACTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 7 0.22
10 9 0.28
11 16 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:714184 original size:30 final size:30
Alignment explanation
Indices: 714108--714176 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
714098 AAATTTAATT
* * *
714108 AAATATAATAAA-AAATAAAAATATATTTA
1 AAATATTATAAATAATTTAAAATATATTTA
* * *
714137 AAATTTTTTAAATAATTTAAAATATTTTTA
1 AAATATTATAAATAATTTAAAATATATTTA
714167 AAATATTATA
1 AAATATTATA
714177 CTTAATTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
AAATATTATAAATAATTTAAAATATATTTA
Found at i:731275 original size:4 final size:4
Alignment explanation
Indices: 731266--731292 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
731256 TTGAGCCAGT
731266 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
731293 TGCAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:756074 original size:20 final size:21
Alignment explanation
Indices: 756044--756082 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
756034 CTGAATTCAG
756044 TAAATTTTTTATATATTTAAT
1 TAAATTTTTTATATATTTAAT
*
756065 TAAA-TTTTTATATTTTTA
1 TAAATTTTTTATATATTTA
756083 TTTTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TAAATTTTTTATATATTTAAT
Found at i:757342 original size:30 final size:30
Alignment explanation
Indices: 757268--757364 Score: 119
Period size: 30 Copynumber: 3.3 Consensus size: 30
757258 TTTAAAAAAA
* *
757268 TTAAATAAGTTTTTATACTTTTA--TTAGG
1 TTAAATAAGTTTTTATATTTTTATTTTAAG
* *
757296 TTCAATCAAATTTTTATATTTTTATTTTAAG
1 TTAAAT-AAGTTTTTATATTTTTATTTTAAG
757327 TTAAATAAGTTTTTATATTTTTATTTTAAAG
1 TTAAATAAGTTTTTATATTTTTATTTT-AAG
757358 -TAAATAA
1 TTAAATAA
757365 ACTTTGATGG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 5 0.08
29 15 0.25
30 27 0.46
31 12 0.20
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (30 bp):
TTAAATAAGTTTTTATATTTTTATTTTAAG
Found at i:772724 original size:2 final size:2
Alignment explanation
Indices: 772717--772742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
772707 AATTAACAAA
772717 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
772743 GGTACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:778158 original size:25 final size:25
Alignment explanation
Indices: 778122--778179 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
778112 AAAAATAATT
*
778122 CACAAAAT-TTAAGTAAACAATAT-C
1 CACAAAATATTAAGTAAA-AAAATCC
*
778146 CACAAAATATTAATTAAAAAAATCC
1 CACAAAATATTAAGTAAAAAAATCC
778171 CACAAAATA
1 CACAAAATA
778180 CCATCTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.59, C:0.17, G:0.02, T:0.22
Consensus pattern (25 bp):
CACAAAATATTAAGTAAAAAAATCC
Found at i:784305 original size:15 final size:15
Alignment explanation
Indices: 784252--784302 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
784242 CATAGGTGAA
*
784252 TTTTACTTATTTATGTT
1 TTTTATTTATTTA--TT
*
784269 TTTTATTTATATATT
1 TTTTATTTATTTATT
784284 TTTTATTTATTTGATT
1 TTTTATTTATTT-ATT
784300 TTT
1 TTT
784303 ATTATTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.43
16 6 0.20
17 11 0.37
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (15 bp):
TTTTATTTATTTATT
Found at i:784311 original size:15 final size:15
Alignment explanation
Indices: 784268--784309 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
784258 TTATTTATGT
*
784268 TTTTTATTTATAT-A
1 TTTTTATTTATTTGA
784282 TTTTTTATTTATTTGA
1 -TTTTTATTTATTTGA
784298 TTTTTA-TTATTT
1 TTTTTATTTATTT
784310 TGTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 18 0.72
16 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTATTTATTTGA
Found at i:819348 original size:14 final size:14
Alignment explanation
Indices: 819292--819351 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
819282 AATTTGAATC
819292 ATTATATTTT-AAA
1 ATTATATTTTAAAA
819305 A-TATATTATATAAAA
1 ATTATATT-T-TAAAA
* * *
819320 TTTAAAATTTCAAAA
1 ATT-ATATTTTAAAA
819335 ATTATATTTTAAAA
1 ATTATATTTTAAAA
819349 ATT
1 ATT
819352 TTAAAACTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
12 6 0.17
13 2 0.06
14 13 0.36
15 9 0.25
16 2 0.06
17 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATATTTTAAAA
Found at i:821989 original size:27 final size:28
Alignment explanation
Indices: 821957--822021 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
821947 AAATTATAAT
*
821957 ACGTCATATT-CAAAAAAATATTGTTAC
1 ACGTCATATTAAAAAAAAATATTGTTAC
* * *
821984 ATGTCATATTAAAAAAAAATGTTGTTAT
1 ACGTCATATTAAAAAAAAATATTGTTAC
822012 ACGTCATATT
1 ACGTCATATT
822022 TAAGATGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (28 bp):
ACGTCATATTAAAAAAAAATATTGTTAC
Found at i:822213 original size:81 final size:84
Alignment explanation
Indices: 822113--822268 Score: 192
Period size: 83 Copynumber: 1.9 Consensus size: 84
822103 TTGTTGAGTC
822113 AAAAAAAATTAATACACATT-ATATTTAAGATATTTAACTTCAAAAGTTTATATATCAACGAAAT
1 AAAAAAAATTAATACACATTCATATTTAAGATATTTAACTTCAAAAGTTTATATATCAACGAAAT
822177 ATAAAGATACACAATATTG
66 ATAAAGATACACAATATTG
* * * * * * * * **
822196 AAAAAAAATT-AT-TACATTCCATGTTTGAGGTGTTTAACTTCAAGAGTTTATATCTTAGTGAAA
1 AAAAAAAATTAATACACATT-CATATTTAAGATATTTAACTTCAAAAGTTTATATATCAACGAAA
822259 TATAAAGATA
65 TATAAAGATA
822269 GAAACCAAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
81 5 0.08
82 2 0.03
83 54 0.89
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.35
Consensus pattern (84 bp):
AAAAAAAATTAATACACATTCATATTTAAGATATTTAACTTCAAAAGTTTATATATCAACGAAAT
ATAAAGATACACAATATTG
Found at i:822346 original size:127 final size:127
Alignment explanation
Indices: 822196--822463 Score: 321
Period size: 127 Copynumber: 2.1 Consensus size: 127
822186 CACAATATTG
* * *
822196 AAAAAAAATTATTACATTCCATGTTTGAGGTGTTTAA-CTTCAAGAGTTTATA-TCTTAGTGAAA
1 AAAAAAAATTATTACAATCCATGTTTAAGGTGTTTAACCTTCAAGAGTTTATATTC-TAATGAAA
* * * * *
822259 TATAAAGATAGAA-ACCAAGTTACACGTCATG-TTGAAAAAAAAAATTGTTATACACTATATTTA
65 TA-AAAGATA-AATACCAAGTTACACGACA-GATTAAAAAAAAAAATTGTTACACACCATATTGA
822322 A
127 A
* * *
822323 AAAAAAAATTATTACACAT-CATGTTTAAGGTGTTTAACCTTCAATATTTTATGTTCTAATGAAA
1 AAAAAAAATTATTACA-ATCCATGTTTAAGGTGTTTAACCTTCAAGAGTTTATATTCTAATGAAA
* * *
822387 TACAAGATAAATACTAAGTTACACGACAGATTAAAAAAAAAAATTGTTACACACCATGTTGAA
65 TAAAAGATAAATACCAAGTTACACGACAGATTAAAAAAAAAAATTGTTACACACCATATTGAA
*
822450 AAAAAAAGTTATTA
1 AAAAAAAATTATTA
822464 TTTAATTCTA
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
126 3 0.02
127 94 0.78
128 22 0.18
129 2 0.02
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (127 bp):
AAAAAAAATTATTACAATCCATGTTTAAGGTGTTTAACCTTCAAGAGTTTATATTCTAATGAAAT
AAAAGATAAATACCAAGTTACACGACAGATTAAAAAAAAAAATTGTTACACACCATATTGAA
Found at i:822349 original size:28 final size:28
Alignment explanation
Indices: 822278--822350 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
822268 AGAAACCAAG
* * *
822278 TTACACGTCATGTTGAAAAAAAAAATTG
1 TTACACATCATGTTTAAAAAAAAAATTA
* *
822306 TTATACA-CTATATTTAAAAAAAAAATTA
1 TTACACATC-ATGTTTAAAAAAAAAATTA
822334 TTACACATCATGTTTAA
1 TTACACATCATGTTTAA
822351 GGTGTTTAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
27 1 0.03
28 34 0.94
29 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (28 bp):
TTACACATCATGTTTAAAAAAAAAATTA
Found at i:825427 original size:21 final size:21
Alignment explanation
Indices: 825401--825443 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
825391 TAATACTTAA
** *
825401 AAAAATTTTAAATTATTTTTT
1 AAAAATTAAAAATAATTTTTT
825422 AAAAATTAAAAATAATTTTTT
1 AAAAATTAAAAATAATTTTTT
825443 A
1 A
825444 TTTATATCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAAATTAAAAATAATTTTTT
Found at i:827601 original size:6 final size:6
Alignment explanation
Indices: 827592--827620 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
827582 GAATTCTTTT
827592 TATTAA TATTAA TATTAA TATTAA TATTA
1 TATTAA TATTAA TATTAA TATTAA TATTA
827621 CTCACATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:828322 original size:17 final size:17
Alignment explanation
Indices: 828300--828335 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
828290 ACGTGTTATT
828300 TATTAAATATGAATTAA
1 TATTAAATATGAATTAA
828317 TATTAAATATGAATTAA
1 TATTAAATATGAATTAA
828334 TA
1 TA
828336 ATGAATAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TATTAAATATGAATTAA
Found at i:828342 original size:17 final size:17
Alignment explanation
Indices: 828303--828342 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
828293 TGTTATTTAT
*
828303 TAAATATGAATTAATAT
1 TAAATATGAATTAATAA
828320 TAAATATGAATTAATAA
1 TAAATATGAATTAATAA
*
828337 TGAATA
1 TAAATA
828343 ATCACAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
TAAATATGAATTAATAA
Found at i:830044 original size:161 final size:161
Alignment explanation
Indices: 829856--830173 Score: 510
Period size: 161 Copynumber: 2.0 Consensus size: 161
829846 CTTGTACCGC
* * * *
829856 TTTAGATGTTTGAATTGAAGCTTGAAGATTATTAGAAACGTTTTGGTTTTTGGTCATTCGAGTTT
1 TTTAGATGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTCGTCATTCAAGTTT
* * * * * *
829921 AGCTAGAGAATCTGGTTTGTAACTTGTAGTAAGGTAGAAAAGTGGTCTGCAGGTTGAGCCACTGA
66 AGCTAGACAATCTGGTTTGTAACGTGTAATAAGGAAGAAAAGTGGTCTGCAGGTAGAGCCACCGA
*
829986 GCTCAGTTGCCTTCAAATTCGCTCCACGACA
131 GCACAGTTGCCTTCAAATTCGCTCCACGACA
*
830017 TTTAGGTGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTCGTCATTCAAGTTT
1 TTTAGATGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTCGTCATTCAAGTTT
*
830082 AGCTAGACAATCTGGTTTGTAACGTGTAATAAGGAAGAAAAGTGGTTTGCAGGTAGAGCCACCGA
66 AGCTAGACAATCTGGTTTGTAACGTGTAATAAGGAAGAAAAGTGGTCTGCAGGTAGAGCCACCGA
*
830147 GCACAGTTGCCTTCAAATTTGCTCCAC
131 GCACAGTTGCCTTCAAATTCGCTCCAC
830174 AACAGTCTAT
Statistics
Matches: 143, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
161 143 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (161 bp):
TTTAGATGTTTGAATTGAAGCTTGAAGATTATAAGAAAAGTTTTGGTTTTTCGTCATTCAAGTTT
AGCTAGACAATCTGGTTTGTAACGTGTAATAAGGAAGAAAAGTGGTCTGCAGGTAGAGCCACCGA
GCACAGTTGCCTTCAAATTCGCTCCACGACA
Found at i:834294 original size:29 final size:29
Alignment explanation
Indices: 834219--834296 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
834209 TTATTTTAAA
* *
834219 AAATTAAATAAATTTTTAATATTTTATTC
1 AAATTAAATAATTTTTTTATATTTTATTC
* * * *
834248 AATTTAATTAAATATTTTTAT-TTTTATTTT
1 AAATTAAAT-AATTTTTTTATATTTTA-TTC
834278 AAATTAAATAATTTTTTTA
1 AAATTAAATAATTTTTTTA
834297 ATTAATAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
AAATTAAATAATTTTTTTATATTTTATTC
Found at i:834990 original size:30 final size:29
Alignment explanation
Indices: 834954--835013 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
834944 CTTTAAAGAC
*
834954 TTAATTGATCTAAAATAAAAATATAAA-ATT
1 TTAATTGAAC-AAAATAAAAA-ATAAATATT
*
834984 TTAATTGAACATAATAAAAAATAAATATT
1 TTAATTGAACAAAATAAAAAATAAATATT
835013 T
1 T
835014 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 13 0.48
30 9 0.33
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TTAATTGAACAAAATAAAAAATAAATATT
Found at i:842772 original size:2 final size:2
Alignment explanation
Indices: 842765--842797 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
842755 AGGCAATATG
842765 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
842798 TAAACATCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:852749 original size:26 final size:26
Alignment explanation
Indices: 852692--852804 Score: 88
Period size: 26 Copynumber: 4.4 Consensus size: 26
852682 TAAGCTCACG
* * *
852692 TAAAAAAAATGTTATTATATGTCCTAT
1 TAAAAAAAAT-TTATTATATATCATGT
* *
852719 T-AAAAAAATTTATTGTATGTCATGT
1 TAAAAAAAATTTATTATATATCATGT
* * *
852744 TAAAAATAA-TTATTTTATATAATG-
1 TAAAAAAAATTTATTATATATCATGT
* *
852768 TAGAAAAAAAATTATTACATATCATGT
1 TA-AAAAAAATTTATTATATATCATGT
*
852795 TGAAAAAAAT
1 TAAAAAAAAT
852805 GATCGAAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
24 2 0.03
25 32 0.46
26 33 0.48
27 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (26 bp):
TAAAAAAAATTTATTATATATCATGT
Found at i:852768 original size:25 final size:24
Alignment explanation
Indices: 852694--852804 Score: 78
Period size: 25 Copynumber: 4.3 Consensus size: 24
852684 AGCTCACGTA
* * *
852694 AAAAAAATGTTATTATATGTCCTATT
1 AAAAAAA--TTATTATATATCATGTT
* *
852720 AAAAAAATTTATTGTATGTCATGTT
1 AAAAAAA-TTATTATATATCATGTT
* * *
852745 AAAAATAATTATTTTATATAATGTAGA
1 AAAAA-AATTATTATATATCATGT--T
*
852772 AAAAAAATTATTACATATCATGTT
1 AAAAAAATTATTATATATCATGTT
852796 GAAAAAAAT
1 -AAAAAAAT
852805 GATCGAAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
25 40 0.58
26 24 0.35
27 5 0.07
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.39
Consensus pattern (24 bp):
AAAAAAATTATTATATATCATGTT
Found at i:854581 original size:16 final size:16
Alignment explanation
Indices: 854560--854596 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
854550 TAAGATGGGA
854560 ATTTGAGTTAGTAATG
1 ATTTGAGTTAGTAATG
*
854576 ATTTGAGTTAGTAGTG
1 ATTTGAGTTAGTAATG
854592 ATTTG
1 ATTTG
854597 CCAAAGCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (16 bp):
ATTTGAGTTAGTAATG
Found at i:862456 original size:11 final size:11
Alignment explanation
Indices: 862434--862467 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
862424 AAAAGTGCTT
*
862434 TTGGGTTCAAA
1 TTGGCTTCAAA
*
862445 TTGGCTTTAAA
1 TTGGCTTCAAA
862456 TTGGCTTCAAA
1 TTGGCTTCAAA
862467 T
1 T
862468 AGAAGTTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (11 bp):
TTGGCTTCAAA
Found at i:871060 original size:44 final size:43
Alignment explanation
Indices: 871005--871093 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 43
870995 ATATTTCCTC
*
871005 TAATGCTTTACTGGTTT-TTAATTATATGTGGTAGGTTCTGATGA
1 TAATACTTTACT--TTTGTTAATTATATGTGGTAGGTTCTGATGA
* *
871049 TAATACTTTACTTTTGGTTCATTATATGTGGTAGGTTCTGGTGA
1 TAATACTTTACTTTT-GTTAATTATATGTGGTAGGTTCTGATGA
871093 T
1 T
871094 CAAGCTTCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 3 0.08
44 37 0.93
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.48
Consensus pattern (43 bp):
TAATACTTTACTTTTGTTAATTATATGTGGTAGGTTCTGATGA
Found at i:874667 original size:2 final size:2
Alignment explanation
Indices: 874660--874695 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
874650 ATCATTAGCA
874660 CT CT 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
874696 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:874700 original size:2 final size:2
Alignment explanation
Indices: 874695--874725 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
874685 TCTCTCTCTC
874695 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
874726 CTTTTAGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:879440 original size:90 final size:89
Alignment explanation
Indices: 879346--879681 Score: 264
Period size: 90 Copynumber: 3.7 Consensus size: 89
879336 TAGTGGCACA
* * ** *
879346 GAGCCATATAGGGGAGATCCCTCCCTTCAATGCTCACCTCATCATGAAGGAGGTGAATTTGGTGG
1 GAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCAGGTCATCATGGAGGAGGTGAATTTGGT-G
*
879411 GTTAAAATGCTATGGTGGTCTTATG
65 GTTAAAATGCTATGGTGGTGTTATG
* * * * * * * *
879436 GAGCCACATA-GAGATGAGCCCTTCTTTGAATACTCAGGTCATCATGGAGAAGGTGAGTTTGGTC
1 GAGCCATATAGGGGA-GAGCCCTCCCTTCAATACTCAGGTCATCATGGAGGAGGTGAATTTGGTG
** * * *
879500 GTTATGGA-GAATATGGTAGTGGTATG
65 GTTA-AAATG-CTATGGTGGTGTTATG
** * *
879526 GAGCTGTATAGGGGAGGGCCCTCCCTTCAATACTCGGGTCATCATGGAGGAGGTGAATTTGGTTG
1 GAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCAGGTCATCATGGAGGAGGTGAATTTGG-TG
* * * *
879591 GTTCAAGTACCATGGTGGTGTTATG
65 GTTAAAATGCTATGGTGGTGTTATG
** * * * * ** * *
879616 GAGCCATATAAAGAAGAGCCATCCCTTGAATACTCCA-ATCATTGTGGAAGAGATGAATTTGGTG
1 GAGCCATATAGGGGAGAGCCCTCCCTTCAATACT-CAGGTCATCATGGAGGAGGTGAATTTGGTG
879680 GT
65 GT
879682 GGAATGGAGC
Statistics
Matches: 185, Mismatches: 54, Indels: 15
0.73 0.21 0.06
Matches are distributed among these distances:
89 12 0.06
90 165 0.89
91 8 0.04
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (89 bp):
GAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCAGGTCATCATGGAGGAGGTGAATTTGGTGG
TTAAAATGCTATGGTGGTGTTATG
Found at i:879539 original size:180 final size:180
Alignment explanation
Indices: 879279--879650 Score: 456
Period size: 180 Copynumber: 2.1 Consensus size: 180
879269 AAGAGCCCCG
* * * * *
879279 CCTTGGATACTCAGGTCGTTATGGAGGAGGTGAATTTGGTTACTATGGAGAATATGGTAGTGGCA
1 CCTTGAATACTCAGGTCATCATGGAGAAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGCA
* *
879344 CAGAGCCATATAGGGGAGATCCCTCCCTTCAATGCTCACCTCATCATGAAGGAGGTGAATTTGGT
66 CAGAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCACCTCATCATGAAGGAGGTGAATTTGGT
* * * * * *
879409 GGGTTAAAATGCTATGGTGGTCTTATGGAGCCACATAGAGATGAGCCCTT
131 GGGTTAAAATACCATGGTGGTCTTATGGAGCCACATAAAGAAGAGCCATC
* * ** *
879459 CTTTGAATACTCAGGTCATCATGGAGAAGGTGAGTTTGGTCGTTATGGAGAATATGGTAGTGGTA
1 CCTTGAATACTCAGGTCATCATGGAGAAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGCA
** ** * *** *
879524 TGGAGCTGTATAGGGGAGGGCCCTCCCTTCAATACTCGGGTCATCATGGAGGAGGTGAATTTGGT
66 CAGAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCACCTCATCATGAAGGAGGTGAATTTGGT
* * * * *
879589 TGGTTCAAGTACCATGGTGGTGTTATGGAGCCATATAAAGAAGAGCCATC
131 GGGTTAAAATACCATGGTGGTCTTATGGAGCCACATAAAGAAGAGCCATC
879639 CCTTGAATACTC
1 CCTTGAATACTC
879651 CAATCATTGT
Statistics
Matches: 159, Mismatches: 33, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
180 159 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (180 bp):
CCTTGAATACTCAGGTCATCATGGAGAAGGTGAATTTGGTCACTATGGAGAATATGGTAGTGGCA
CAGAGCCATATAGGGGAGAGCCCTCCCTTCAATACTCACCTCATCATGAAGGAGGTGAATTTGGT
GGGTTAAAATACCATGGTGGTCTTATGGAGCCACATAAAGAAGAGCCATC
Found at i:880190 original size:17 final size:16
Alignment explanation
Indices: 880168--880221 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
880158 TTGTTTGATG
880168 TTTTTATTATAATAAAA
1 TTTTTATTA-AATAAAA
880185 TTTTTA-TAAATTAATAA
1 TTTTTATTAAA-TAA-AA
* *
880202 TTTTGATTAAATAATA
1 TTTTTATTAAATAAAA
880218 TTTT
1 TTTT
880222 AAATTGATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 2 0.06
16 10 0.31
17 16 0.50
18 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTTTATTAAATAAAA
Found at i:880423 original size:14 final size:14
Alignment explanation
Indices: 880392--880421 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
880382 AAAATATAAA
880392 TTTAATATTATTTT
1 TTTAATATTATTTT
880406 TTTAA-ATTATTTT
1 TTTAATATTATTTT
880419 TTT
1 TTT
880422 TATTTTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTAATATTATTTT
Found at i:881628 original size:19 final size:19
Alignment explanation
Indices: 881606--881643 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
881596 AAAATTATTT
881606 TTAAAAATTAATTAATAAA
1 TTAAAAATTAATTAATAAA
*
881625 TTAAAAATTAATTCATAAA
1 TTAAAAATTAATTAATAAA
881644 AATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAAAAATTAATTAATAAA
Found at i:889551 original size:18 final size:18
Alignment explanation
Indices: 889525--889566 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
889515 ATCACATCAT
*
889525 AAATGTATAAATATTTTTA
1 AAAT-TATAAATATTTATA
889544 AAATTATAAATATTTATA
1 AAATTATAAATATTTATA
889562 AAATT
1 AAATT
889567 TTATATCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AAATTATAAATATTTATA
Found at i:896554 original size:24 final size:23
Alignment explanation
Indices: 896526--896570 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
896516 TAAAATTAAT
**
896526 TAAAATATTTATTTAGTTTAAAAA
1 TAAAATAAATATTTA-TTTAAAAA
896550 TAAAATAAATATTTATTTAAA
1 TAAAATAAATATTTATTTAAA
896571 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAAATAAATATTTATTTAAAAA
Found at i:903019 original size:19 final size:20
Alignment explanation
Indices: 902993--903033 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
902983 GTATAATACA
*
902993 TAAAAAAATTTTAAAT-TATT
1 TAAAAAAA-ATTAAATATATT
903013 TAAAAAAAATTAAATATATT
1 TAAAAAAAATTAAATATATT
903033 T
1 T
903034 TTTTCTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAAAAATTAAATATATT
Found at i:912992 original size:4 final size:4
Alignment explanation
Indices: 912969--913003 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
912959 TATTATTTTA
*
912969 AATT AAGTT AATT AACT AATT AATT AATT AATT AA
1 AATT AA-TT AATT AATT AATT AATT AATT AATT AA
913004 AATATCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (4 bp):
AATT
Found at i:913325 original size:2 final size:2
Alignment explanation
Indices: 913318--913369 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
913308 ACTTGTCCAA
913318 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
913360 AT AT AT AT AT
1 AT AT AT AT AT
913370 CCACTTGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:914397 original size:16 final size:16
Alignment explanation
Indices: 914358--914397 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
914348 TTCATCTCTC
914358 ATTTT-TTTTTATTTG
1 ATTTTATTTTTATTTG
**
914373 ATTCAATTTTTATTTG
1 ATTTTATTTTTATTTG
914389 ATTTTATTT
1 ATTTTATTT
914398 ATTTATTAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (16 bp):
ATTTTATTTTTATTTG
Found at i:914481 original size:13 final size:13
Alignment explanation
Indices: 914443--914483 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
914433 TATGTGTTAG
914443 TTATAAATTATTT
1 TTATAAATTATTT
914456 TT-TAAACTT-TTT
1 TTATAAA-TTATTT
*
914468 TTATAATTTATTT
1 TTATAAATTATTT
914481 TTA
1 TTA
914484 ATTATAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATAAATTATTT
Found at i:920727 original size:23 final size:22
Alignment explanation
Indices: 920700--920742 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
920690 TTTTCTATAT
*
920700 TCTTTTTATTTTATCTATTTTTA
1 TCTTTTTATTGTATCT-TTTTTA
*
920723 TCTTTTTCTTGTATCTTTTT
1 TCTTTTTATTGTATCTTTTT
920743 ACTATTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (22 bp):
TCTTTTTATTGTATCTTTTTTA
Found at i:920811 original size:27 final size:27
Alignment explanation
Indices: 920745--920813 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
920735 ATCTTTTTAC
* *
920745 TATTCATCTACTTCTGACAATTAAATG
1 TATTCATCTACTTCCGACAATTAAATA
* **
920772 TATCCAT-TGACTTCCGGTAATTAAATA
1 TATTCATCT-ACTTCCGACAATTAAATA
920799 TATTCATCTACTTCC
1 TATTCATCTACTTCC
920814 ACTGGTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (27 bp):
TATTCATCTACTTCCGACAATTAAATA
Found at i:920951 original size:21 final size:23
Alignment explanation
Indices: 920910--920952 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
920900 TATTAGAATA
920910 GTAATTAGTATACCATCACAATT
1 GTAATTAGTATACCATCACAATT
*
920933 GTAATTATTAT-CC-TCACAAT
1 GTAATTAGTATACCATCACAAT
920953 GTCCATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (23 bp):
GTAATTAGTATACCATCACAATT
Found at i:926815 original size:3 final size:3
Alignment explanation
Indices: 926807--926846 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
926797 AAAAATACAG
926807 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
926847 GCATAAACTA
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:930251 original size:30 final size:31
Alignment explanation
Indices: 930217--930301 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 31
930207 ATTATAAGTT
* *
930217 CTTATTTGATTCAAAAT-AAAAATATAAAAA
1 CTTATTTAATTCAAAATAAAAAAAATAAAAA
*
930247 CTTATTTAATTTAAAATAAAAAAAATAAAAA
1 CTTATTTAATTCAAAATAAAAAAAATAAAAA
* *
930278 --TATTGAA-T-GAAATAAAAAAAATAA
1 CTTATTTAATTCAAAATAAAAAAAATAA
930302 CTTATTCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
27 15 0.31
28 1 0.02
29 6 0.12
30 15 0.31
31 12 0.24
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (31 bp):
CTTATTTAATTCAAAATAAAAAAAATAAAAA
Found at i:933441 original size:18 final size:19
Alignment explanation
Indices: 933420--933457 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
933410 GATATTTATC
*
933420 TCTAATTTAATATT-TTAA
1 TCTAATTTAAAATTATTAA
*
933438 TCTACTTTAAAATTATTAA
1 TCTAATTTAAAATTATTAA
933457 T
1 T
933458 GAATTCCCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
TCTAATTTAAAATTATTAA
Found at i:934050 original size:208 final size:206
Alignment explanation
Indices: 933687--934067 Score: 504
Period size: 208 Copynumber: 1.8 Consensus size: 206
933677 GAGATTATTA
* * ** *
933687 TAAAGTGATTGTTAGAAATGTAATTATTGAAAATGTTATTGTTAAGAAGATAATATTATGGCGTT
1 TAAAGTGATTGTTAGAAATGTAATTATTGAAAATG-TATTATTAAAAAGATAATATTATAACATT
* *
933752 TGATGTATATGAGAAAGTATTGATTAAAATACTGAGAAAATAATAATGTAATGTTTTGTTTATAA
65 TGATGTATATGAGAAAGTATTGATTAAAATACTGAGAAAAGAATAATGTAATGTTTGGTTTATAA
*
933817 ATATTTTACTAGAAATGTTATATTAATTTTCAAAATTACCATTGGCATTTGGTATCTTACAATAT
130 ATACTTTACTAGAAATG-TATATTAATTTTCAAAATTACCATTGGCATTTGGTATCTTACAATAT
933882 AATGGGATTGCTG
194 AATGGGATTGCTG
* * *
933895 TAAAGTGATTGTTAGGAATGTAATTATTAAGAACATG-ATTATTAAAAAGATAATATTGTAACAT
1 TAAAGTGATTGTTAGAAATGTAATTATT--GAAAATGTATTATTAAAAAGATAATATTATAACAT
* *
933959 TT-A-GTATACATGATAAAGTATTGATTAAAATACT-A-AAAAGACAGTATTGTAATGTTTGGTT
64 TTGATGTAT--ATGAGAAAGTATTGATTAAAATACTGAGAAAAGA-A-TAATGTAATGTTTGGTT
*
934020 TATAAATACTTTACTAAGAATATG-ATATTAATTTTTAAAATTACCATT
125 TATAAATACTTTACT-AGAA-ATGTATATTAATTTTCAAAATTACCATT
934068 ATGTATGAAA
Statistics
Matches: 151, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
206 9 0.06
207 3 0.02
208 126 0.83
209 4 0.03
210 9 0.06
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (206 bp):
TAAAGTGATTGTTAGAAATGTAATTATTGAAAATGTATTATTAAAAAGATAATATTATAACATTT
GATGTATATGAGAAAGTATTGATTAAAATACTGAGAAAAGAATAATGTAATGTTTGGTTTATAAA
TACTTTACTAGAAATGTATATTAATTTTCAAAATTACCATTGGCATTTGGTATCTTACAATATAA
TGGGATTGCTG
Found at i:939780 original size:4 final size:4
Alignment explanation
Indices: 939771--939799 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
939761 CATTGAACAT
939771 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
939800 ATATTAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:940073 original size:22 final size:22
Alignment explanation
Indices: 940039--940095 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
940029 CTTTTTTTGG
*
940039 ATTTTTTTAAAAAATTTA-TATT
1 ATTTTTTTAAAAAATTGATTA-T
940061 ATTATTTTTAAAAAATTGATTAT
1 ATT-TTTTTAAAAAATTGATTAT
940084 ATTTTTTTAAAA
1 ATTTTTTTAAAA
940096 GTTATTACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 12 0.38
23 18 0.56
24 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTTTTTAAAAAATTGATTAT
Found at i:942080 original size:26 final size:25
Alignment explanation
Indices: 942051--942103 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
942041 TATTTTTAAC
*
942051 TAATTTATTAATAATATAATAATATT
1 TAATTTATTAATAATAT-ATAAAATT
*
942077 TAATTTATTGATAATATATAAAATT
1 TAATTTATTAATAATATATAAAATT
942102 TA
1 TA
942104 TGTACTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATTTATTAATAATATATAAAATT
Found at i:953923 original size:500 final size:497
Alignment explanation
Indices: 953235--954376 Score: 1463
Period size: 500 Copynumber: 2.3 Consensus size: 497
953225 CAATACTAAC
* * *
953235 TTTTAACTATAATTATTTTTATCTTTATTATTTTTATTT-AACATAAAAATTTAAATATCGTTAC
1 TTTTAACTATAATTATTTTTATCTTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAC
* * * *
953299 ATATTTTTAGCCCGATAATATAAATATAAATACTTATTTTTTATTAAAATTAGACTTTTTTACTT
66 ATA-TTTTAGCTCAATAATATAAATATAAATACTTATTTTTCATTAAAATTAGACTATTTTACTT
* *
953364 AATTAATTTATTACGTTAACTCTCACACATTTACGTTAATATTTAAAATTTAGTTATTCCACCTT
130 AATTAACTTATTACGTTAACTCTCACACATTTACGTTAATATTTAAAATTTAATTATTCCACCTT
* * * * *
953429 TATAAGTTTTTACGTCAACTATTATAATTTTACGTCAAGATTTATCTATGCTAATTTTGAACTAT
195 TACAAGTTCTTACATCAACTATTACAATTTTACGTCAAGATTTATCTATGCTAATTTTAAACTAT
*
953494 AATTA-TTTAT-ATTATTATTATTTATTTAAAAAATAAAATTTATATATCGTTAAACACTTTTAG
260 AATTATTTTATCATTATTATT-TTTATTTAAAAAATAAAACTTATATATCGTTAAACACTTTTAG
* * *
953557 TCCAAGAATATATATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTTTACTCAATAGAC
324 TCCAAGAATATAAATTTAAATATTTATTTTTCAATAAAATTA-A-ATTTTTTTTACTCAATAGAC
* * *
953622 TTGTTACGTTAACTCTCATACATTTACGTTAAGATTTAAAATTTAGTTATTCTACT-TTTATAAA
387 TTATTACGTTAACCCTCATACATTTACGTTAAGATTTAAAATTTAATTATTCTA-TATTTAT-AA
* * * *
953686 TTTTTACATCAACTCTTATAGTTTTACGTTAAAACTTACT-TATGTCAA
450 GTTTGACATCAACTCTTATAATTTTACGTTAAAA-TTACTCTATATCAA
*
953734 TTTTATACTATAATTATTTTTATCTTTATTA-TTTTATTTAAAAATTAAAATTTATATATTGTTA
1 TTTTA-ACTATAATTATTTTTATCTTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTA
* * *
953798 CATTATTTTAGCTTAATAATATAAATATAAATACTTATTTTTCGTTAAAATTAGACTATTTTGCT
65 CA-TATTTTAGCTCAATAATATAAATATAAATACTTATTTTTCATTAAAATTAGACTATTTTACT
* *
953863 TAATTAACTTATTATGTTAACTCTCACATATTTACGTTAATATTTAAAATTTAATTATTCCACCT
129 TAATTAACTTATTACGTTAACTCTCACACATTTACGTTAATATTTAAAATTTAATTATTCCACCT
* * * * * *
953928 TTACAAGTTCTTACATTAATTCTTACAGTTTTACGTCAAGGTTTATCTATGTTAATTTTAAACTA
194 TTACAAGTTCTTACATCAACTATTACAATTTTACGTCAAGATTTATCTATGCTAATTTTAAACTA
* * * *
953993 TAATTATTTTTATCCTTATTATTTTTATTTAAAAATTAAAACTTATATATCGTTAAATATTTTTA
259 TAATTA-TTTTATCATTATTATTTTTATTTAAAAAATAAAACTTATATATCGTTAAACACTTTTA
* * * * *
954058 TTTCAAGAATATAAATTTAAATATTTATTTTTTAATAAAATTAAATTTTTTTTACTTAATTGACT
323 GTCCAAGAATATAAATTTAAATATTTATTTTTCAATAAAATTAAATTTTTTTTACTCAATAGACT
* * * *
954123 TATTATGTTAACCCTCATATATTTATGTTAAGATTTAAAATTTAATTATTTTATATTTATAAGTT
388 TATTACGTTAACCCTCATACATTTACGTTAAGATTTAAAATTTAATTATTCTATATTTATAAGTT
* * * ** *
954188 TGACGTCAATTCTTATAATTTTACGTTAAGATTTTTCTATATCTA
453 TGACATCAACTCTTATAATTTTACGTTAAAATTACTCTATATCAA
* * *
954233 TTTTAAACTATAATTATTTTAATCCTTATTATTCTTTGTTTAAAAATTAAAATTTATATATCGTT
1 TTTT-AACTATAATTATTTTTATCTTTATTATT-TTTATTTAAAAATTAAAATTTATATATCGTT
* * * * * * * * * *
954298 AAACACTTTTTGTCTGAA-AATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTT
64 ACATA-TTTTAG-CTCAATAATATAAATATAAATACTTATTTTTCATTAAAATTAGA-CTATTTT
*
954362 ATTTAATTAA-TTATT
126 ACTTAATTAACTTATT
954377 TCAATTCTTA
Statistics
Matches: 556, Mismatches: 73, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
498 3 0.01
499 77 0.14
500 293 0.53
501 77 0.14
502 98 0.18
503 8 0.01
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.50
Consensus pattern (497 bp):
TTTTAACTATAATTATTTTTATCTTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAC
ATATTTTAGCTCAATAATATAAATATAAATACTTATTTTTCATTAAAATTAGACTATTTTACTTA
ATTAACTTATTACGTTAACTCTCACACATTTACGTTAATATTTAAAATTTAATTATTCCACCTTT
ACAAGTTCTTACATCAACTATTACAATTTTACGTCAAGATTTATCTATGCTAATTTTAAACTATA
ATTATTTTATCATTATTATTTTTATTTAAAAAATAAAACTTATATATCGTTAAACACTTTTAGTC
CAAGAATATAAATTTAAATATTTATTTTTCAATAAAATTAAATTTTTTTTACTCAATAGACTTAT
TACGTTAACCCTCATACATTTACGTTAAGATTTAAAATTTAATTATTCTATATTTATAAGTTTGA
CATCAACTCTTATAATTTTACGTTAAAATTACTCTATATCAA
Found at i:954201 original size:250 final size:250
Alignment explanation
Indices: 953121--954376 Score: 1283
Period size: 251 Copynumber: 5.0 Consensus size: 250
953111 TATTATTATC
* * * ** *
953121 ACTTATTACGTTAACTCTCACATATTTACGTTAAAATTT-TAATTTTTTTA-TCTCACTTTTATA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTC-CACCTTTAT-
* ** * * * * * **
953184 AAATTTTATGTTAATTTTTACAATTTTACGTCAA-ACCTTT-TCAATACTAACTTTT-AACTATA
64 AAGTTTTACATCAACTCTTATAATTTTACGTCAAGA--TTTATCTATGTTAA-TTTTAAACTATA
* * * * * *
953246 ATTATTTTTATCTTTATTATTTTTATTT-AACATAAAAATTTAAATATCGTTACATATTTTTAGC
126 ATTATTTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATATTTTTAGT
* * * * * * *
953310 CCGATAATATAAATATAAATACTTATTTTTTATTAAAATTAGA-CTTTTTTACTTAATTA
191 TCAAGAATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTACTTAATTA
* * *
953369 ATTTATTACGTTAACTCTCACACATTTACGTTAATATTTAAAATTTAGTTATTCCACCTTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCCACCTTTATAA
* * * *
953434 GTTTTTACGTCAACTATTATAATTTTACGTCAAGATTTATCTATGCTAATTTTGAACTATAATTA
66 G-TTTTACATCAACTCTTATAATTTTACGTCAAGATTTATCTATGTTAATTTTAAACTATAATTA
* * * * *
953499 --TTTAT-ATTATTATTATTTATTTAAAAAATAAAATTTATATATCGTTAAACACTTTTAGTCCA
130 TTTTTATCCTTATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATATTTTTAGTTCA
* * *
953561 AGAATATATATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTTTACTCAA-TA
194 AGAATATAAATTTAAATATTTATTTTTTACTAAAATTAGA--TTTTTTTTACTTAATTA
* * * * *
953619 GACTTGTTACGTTAACTCTCATACATTTACGTTAAGATTTAAAATTTAGTTATTCTACTTTTATA
1 -ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCCACCTTTAT-
* * * * * * *
953684 AATTTTTACATCAACTCTTATAGTTTTACGTTAAAACTTA-CTTATGTCAATTTTATACTATAAT
64 AAGTTTTACATCAACTCTTATAATTTTACGTCAAGATTTATC-TATGTTAATTTTAAACTATAAT
* * *
953748 TATTTTTATCTTTATTA-TTTTATTTAAAAATTAAAATTTATATATTGTTACAT-TATTTTAGCT
128 TATTTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATAT-TTTTAG-T
* * * *** * * *
953811 T-AATAATATAAATATAAATACTTATTTTTCGTTAAAATTAGA-CTATTTTGCTTAATTA
191 TCAAGAATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTACTTAATTA
* * * *
953869 ACTTATTATGTTAACTCTCACATATTTACGTTAATATTTAAAATTTAATTATTCCACCTTTACAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCCACCTTTATAA
* * * * *
953934 GTTCTTACATTAATTCTTACAGTTTTACGTCAAGGTTTATCTATGTTAATTTTAAACTATAATTA
66 GTT-TTACATCAACTCTTATAATTTTACGTCAAGATTTATCTATGTTAATTTTAAACTATAATTA
* *
953999 TTTTTATCCTTATTATTTTTATTTAAAAATTAAAACTTATATATCGTTAAATATTTTTATTTCAA
130 TTTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATATTTTTAGTTCAA
* * *
954064 GAATATAAATTTAAATATTTATTTTTTAATAAAATTAAATTTTTTTTACTTAATTG
195 GAATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTACTTAATTA
* * * * * ** **
954120 ACTTATTATGTTAACCCTCATATATTTATGTTAAGATTTAAAATTTAATTATTTTATATTTATAA
1 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCCACCTTTATAA
* * * * * *
954185 GTTTGACGTCAATTCTTATAATTTTACGTTAAGATTTTTCTATATCT-ATTTTAAACTATAATTA
66 GTTTTACATCAACTCTTATAATTTTACGTCAAGATTTATCTATGT-TAATTTTAAACTATAATTA
* * *
954249 TTTTAATCCTTATTATTCTTTGTTTAAAAATTAAAATTTATATATCGTTAAACACTTTTT-GTCT
130 TTTTTATCCTTATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTAAATA-TTTTTAGT-T
* *
954313 GAA-AATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTATTTAATTA
192 CAAGAATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTACTTAATTA
954371 A-TTATT
1 ACTTATT
954377 TCAATTCTTA
Statistics
Matches: 848, Mismatches: 130, Indels: 58
0.82 0.13 0.06
Matches are distributed among these distances:
246 8 0.01
247 12 0.01
248 113 0.13
249 190 0.22
250 152 0.18
251 278 0.33
252 82 0.10
253 7 0.01
254 6 0.01
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (250 bp):
ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAATTATTCCACCTTTATAA
GTTTTACATCAACTCTTATAATTTTACGTCAAGATTTATCTATGTTAATTTTAAACTATAATTAT
TTTTATCCTTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAATATTTTTAGTTCAAG
AATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTTACTTAATTA
Found at i:957201 original size:4 final size:4
Alignment explanation
Indices: 957192--957223 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
957182 TATCTTTTCC
*
957192 ATTA ATTA ATTA ATCA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
957224 TGCAACCTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:964369 original size:110 final size:109
Alignment explanation
Indices: 964232--964444 Score: 313
Period size: 110 Copynumber: 1.9 Consensus size: 109
964222 TAAAATAACT
*
964232 AAATATATTGATTTAGTTACAACTTTCACAATTTATAAATACACATT-TTTTAAAAAAATTAGTC
1 AAATATATTGATTTAGTTACAACTTTCACAATTTACAAATACACATTCTTTT---AAAATTAGTC
964296 AACTCTTACCTAATTT-ATCTTTTATTTAAATTTACTCAAATTAGCA
63 AACTCTTACCTAATTTAATCTTTTATTTAAATTTACTCAAATTAGCA
** ** *
964342 AAATATATTGATTTAGTTACAACTTTCACAATTTACAAATATTCATTCTTTTGCAATTATTCAAC
1 AAATATATTGATTTAGTTACAACTTTCACAATTTACAAATACACATTCTTTTAAAATTAGTCAAC
* *
964407 TCTTATCTAATTTAATTTTTTATTTAAATTTACTCAAA
66 TCTTACCTAATTTAATCTTTTATTTAAATTTACTCAAA
964445 ATTTCTTATG
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
108 22 0.24
109 23 0.25
110 44 0.47
111 4 0.04
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.45
Consensus pattern (109 bp):
AAATATATTGATTTAGTTACAACTTTCACAATTTACAAATACACATTCTTTTAAAATTAGTCAAC
TCTTACCTAATTTAATCTTTTATTTAAATTTACTCAAATTAGCA
Found at i:965896 original size:15 final size:16
Alignment explanation
Indices: 965869--965901 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
965859 ATTTAGTTTC
965869 TTATAATGTAATGTGA
1 TTATAATGTAATGTGA
965885 TTATAA-GTAATGTGA
1 TTATAATGTAATGTGA
965900 TT
1 TT
965902 GTAGAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TTATAATGTAATGTGA
Found at i:966147 original size:33 final size:33
Alignment explanation
Indices: 966103--966190 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
966093 TTTTAATGTC
*
966103 ATATATATTATTTTCATTTCTTATTATAA-TCTT
1 ATATATATTATTTTCATTT-TTAATATAATTCTT
* *
966136 ATATATTTTATTTTTATTTTTAATATAATTTCTT
1 ATATATATTATTTTCATTTTTAATATAA-TTCTT
966170 ATAT-TATATATTTT-ATTTTTA
1 ATATATAT-TATTTTCATTTTTA
966191 TTTTTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 8 0.17
33 26 0.54
34 14 0.29
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (33 bp):
ATATATATTATTTTCATTTTTAATATAATTCTT
Found at i:967615 original size:16 final size:15
Alignment explanation
Indices: 967575--967618 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
967565 TATATTTTTA
*
967575 AATTTT-ATTTAAGT
1 AATTTTAATTTAATT
*
967589 AATTATAATTTAATT
1 AATTTTAATTTAATT
967604 ATATTTTAATTTAAT
1 A-ATTTTAATTTAAT
967619 AAGGTTCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
AATTTTAATTTAATT
Found at i:974589 original size:23 final size:23
Alignment explanation
Indices: 974534--974593 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
974524 TAAAGAAATT
*
974534 AAAATAAAATTATTT-ATTCATA
1 AAAATAAAATTATTTAATTCACA
* *
974556 AAAAGT--TATTATTTAATTTACA
1 AAAA-TAAAATTATTTAATTCACA
974578 AAAATAAAATTATTTA
1 AAAATAAAATTATTTA
974594 TAATAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 8 0.27
22 13 0.43
23 9 0.30
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATAAAATTATTTAATTCACA
Found at i:974777 original size:23 final size:22
Alignment explanation
Indices: 974751--974816 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
974741 AAAATATACA
*
974751 AAAAATTGAATGAA-AAAAAACAT
1 AAAAATT-AATTAACAAAAAA-AT
974774 AAAAATTAATTAACAAAAAAAT
1 AAAAATTAATTAACAAAAAAAT
*
974796 TAAAATTAATTAACAAAAAAA
1 AAAAATTAATTAACAAAAAAA
974817 AATTAAGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 27 0.68
23 13 0.32
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (22 bp):
AAAAATTAATTAACAAAAAAAT
Found at i:974818 original size:18 final size:19
Alignment explanation
Indices: 974774--974822 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 19
974764 AAAAAAACAT
974774 AAAAATTAATTAACAAAAAA
1 AAAAATTAATTAAC-AAAAA
974794 ATTAAAATTAATTAAC-AAAA
1 A--AAAATTAATTAACAAAAA
974814 AAAAATTAA
1 AAAAATTAA
974823 GTAAAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.30
20 6 0.22
22 13 0.48
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATTAATTAACAAAAA
Found at i:978240 original size:23 final size:23
Alignment explanation
Indices: 978188--978240 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
978178 TTTTCTTTAA
* *
978188 TTTAATGTTAAAATTTTTATTTT
1 TTTAATTTTAAAATATTTATTTT
* * *
978211 ATGAATTTTAACATATTTATTTT
1 TTTAATTTTAAAATATTTATTTT
978234 TTTAATT
1 TTTAATT
978241 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTAATTTTAAAATATTTATTTT
Found at i:981704 original size:2 final size:2
Alignment explanation
Indices: 981699--981734 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
981689 TTTTTATCAT
*
981699 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
981735 ACCATTCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:992473 original size:62 final size:62
Alignment explanation
Indices: 992371--992490 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 62
992361 NNNNNNNNNN
* *
992371 AATTTAGAAAGGAGAGTCTTTTAATAATTTGCTTGAAAAAATTAAAAACTTGTGAGAAAATA
1 AATTTAGAAAGGAGAGTCTTTTAATAATTTGATTGAAAAAATTAAAAACATGTGAGAAAATA
* * *
992433 AATTTAGAAAGGGGAGTAC-TTTAATAATTTTATT-AGAAAAATTAATAACATGTGAGAA
1 AATTTAGAAAGGAGAGT-CTTTTAATAATTTGATTGA-AAAAATTAAAAACATGTGAGAA
992491 TAGAGTGGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 1 0.02
62 49 0.96
63 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.33
Consensus pattern (62 bp):
AATTTAGAAAGGAGAGTCTTTTAATAATTTGATTGAAAAAATTAAAAACATGTGAGAAAATA
Found at i:1007133 original size:30 final size:30
Alignment explanation
Indices: 1007058--1007133 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
1007048 TCAAAAAAAT
* * *
1007058 TCAAAAAAGTCTT-TATTTTTTTTTTATGT
1 TCAAATAAGTCTTATATTTTTATTTTATGA
1007087 TC-AATCAAGTCTTTATATTTTTATTTTA-GA
1 TCAAAT-AAGTC-TTATATTTTTATTTTATGA
1007117 TCAAATAAGCTCTTATA
1 TCAAATAAG-TCTTATA
1007134 ATTAATGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 2 0.05
29 7 0.18
30 13 0.33
31 17 0.44
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (30 bp):
TCAAATAAGTCTTATATTTTTATTTTATGA
Found at i:1007289 original size:33 final size:33
Alignment explanation
Indices: 1007247--1007311 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1007237 GCATATTAAG
*
1007247 TCATTATCAATTATAATATGTTAA-TATACCACA
1 TCATCATCAATTATAATATGTTAACT-TACCACA
*
1007280 TCATCATCAATTATAATATTTTAACTTACCAC
1 TCATCATCAATTATAATATGTTAACTTACCAC
1007312 GCTAGCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (33 bp):
TCATCATCAATTATAATATGTTAACTTACCACA
Found at i:1007853 original size:30 final size:30
Alignment explanation
Indices: 1007817--1007914 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
1007807 AGTCATTAAT
*
1007817 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTAAATTTAAAATAAAAA
* *
1007847 TATAAAAATTTATTAAACTCAAAATAAAAGA
1 TATAAAAATTTATTAAATTTAAAATAAAA-A
* * *
1007878 -ATAATAATTTTGATTGAATGT--AATAAAAA
1 TATAA-AAATTT-ATTAAATTTAAAATAAAAA
1007907 TATAAAAA
1 TATAAAAA
1007915 AAAATTCAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
29 3 0.05
30 41 0.75
31 6 0.11
32 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (30 bp):
TATAAAAATTTATTAAATTTAAAATAAAAA
Found at i:1011221 original size:21 final size:21
Alignment explanation
Indices: 1011195--1011249 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1011185 GGGTTTATTT
1011195 GAATTTTTTTCAATAATTCAA
1 GAATTTTTTTCAATAATTCAA
1011216 GAATTTTTTTCAATAATTCAA
1 GAATTTTTTTCAATAATTCAA
1011237 GAATTTTTTTCAA
1 GAATTTTTTTCAA
1011250 GTATTATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (21 bp):
GAATTTTTTTCAATAATTCAA
Found at i:1016881 original size:52 final size:52
Alignment explanation
Indices: 1016803--1016906 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
1016793 AAATCCTTTC
*
1016803 TTTAACATTACTTCCTATGATAGAGAGATTACTATATTAATTAGTTCATACT
1 TTTAACATTACTTCCTATGATAGAGAGATTACTAGATTAATTAGTTCATACT
*
1016855 TTTAACATTACTTCCTATGATAGAGAGATTAGTAGATTAATTAGTTCATACT
1 TTTAACATTACTTCCTATGATAGAGAGATTACTAGATTAATTAGTTCATACT
1016907 AGGTAAATCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (52 bp):
TTTAACATTACTTCCTATGATAGAGAGATTACTAGATTAATTAGTTCATACT
Found at i:1026514 original size:7 final size:7
Alignment explanation
Indices: 1026502--1026526 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1026492 GGCTCTGTGT
1026502 GCAGCAG
1 GCAGCAG
1026509 GCAGCAG
1 GCAGCAG
1026516 GCAGCAG
1 GCAGCAG
1026523 GCAG
1 GCAG
1026527 TATATCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.44, T:0.00
Consensus pattern (7 bp):
GCAGCAG
Found at i:1031263 original size:16 final size:16
Alignment explanation
Indices: 1031242--1031272 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1031232 CTGGTCCTTA
*
1031242 ACTTAGGAAGGGATTT
1 ACTTAGGAAAGGATTT
1031258 ACTTAGGAAAGGATT
1 ACTTAGGAAAGGATT
1031273 CATGTTATTT
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:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
ACTTAGGAAAGGATTT
Found at i:1031425 original size:17 final size:16
Alignment explanation
Indices: 1031385--1031440 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1031375 ATAATATATT
1031385 TTATTTT-TTAAAATA
1 TTATTTTATTAAAATA
**
1031400 TTAAATTATTAAAATAA
1 TTATTTTATTAAAAT-A
1031417 TTATTTTA-T-AAATA
1 TTATTTTATTAAAATA
1031431 TTATCTTTAT
1 TTAT-TTTAT
1031441 GCTTAAACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 5 0.15
15 13 0.39
16 8 0.24
17 7 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTTATTAAAATA
Found at i:1033998 original size:19 final size:19
Alignment explanation
Indices: 1033974--1034012 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1033964 TTTTATTTTA
1033974 AATT-AAATAAATATTTATT
1 AATTAAAAT-AATATTTATT
*
1033993 AATTAAAATATTATTTATT
1 AATTAAAATAATATTTATT
1034012 A
1 A
1034013 TTTTATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAAAATAATATTTATT
Found at i:1034218 original size:20 final size:20
Alignment explanation
Indices: 1034181--1034218 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1034171 AGATTTAATT
*
1034181 AATTTTTTTGAATAATTACA
1 AATTTTTTTGAAAAATTACA
1034201 AATTTTTTT-AAAACATTA
1 AATTTTTTTGAAAA-ATTA
1034219 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTTTTTTGAAAAATTACA
Found at i:1036991 original size:27 final size:27
Alignment explanation
Indices: 1036953--1037006 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1036943 GCTATGCGTC
1036953 CCCACAGTATTATCCACCTACACAAGA
1 CCCACAGTATTATCCACCTACACAAGA
1036980 CCCACAGTATTATCCACCTACACAAGA
1 CCCACAGTATTATCCACCTACACAAGA
1037007 GCATGACAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.19
Consensus pattern (27 bp):
CCCACAGTATTATCCACCTACACAAGA
Found at i:1038929 original size:54 final size:54
Alignment explanation
Indices: 1038870--1038975 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
1038860 CTCCTACATC
* * * *
1038870 TGGTGCAGCATCTTTCAACAGCTCAAAACCTTCCCATTCTACCAGTTTCCAATA
1 TGGTGCAACATCTTTCAACAGCTCAAAACCTTCCAATCCCACCAGTTTCCAATA
** *
1038924 TGGTGCAACATCTTTCAGTAGCTCAAAACCTTCTAATCCCACCAGTTTCCAA
1 TGGTGCAACATCTTTCAACAGCTCAAAACCTTCCAATCCCACCAGTTTCCAA
1038976 CCAAGTGTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.29
Consensus pattern (54 bp):
TGGTGCAACATCTTTCAACAGCTCAAAACCTTCCAATCCCACCAGTTTCCAATA
Found at i:1042556 original size:30 final size:30
Alignment explanation
Indices: 1042520--1042585 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
1042510 GAAGCACTCG
1042520 GCTCCCTTGCCTTGAGGAGCACCATCGAGC
1 GCTCCCTTGCCTTGAGGAGCACCATCGAGC
* * * *
1042550 GCTCCCTTGGCTTGGGGAGCACTATCGAGT
1 GCTCCCTTGCCTTGAGGAGCACCATCGAGC
1042580 GCTCCC
1 GCTCCC
1042586 CTGGTGCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.23
Consensus pattern (30 bp):
GCTCCCTTGCCTTGAGGAGCACCATCGAGC
Found at i:1054650 original size:15 final size:15
Alignment explanation
Indices: 1054626--1054664 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
1054616 TACAATCTTT
*
1054626 TAATTCAAAAAAATA
1 TAATTTAAAAAAATA
1054641 TAATTT-AAAAAATA
1 TAATTTAAAAAAATA
1054655 TAATTTAAAA
1 TAATTTAAAA
1054665 TATTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATTTAAAAAAATA
Found at i:1054664 original size:13 final size:14
Alignment explanation
Indices: 1054633--1054664 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1054623 TTTTAATTCA
1054633 AAAAAATATAATTT
1 AAAAAATATAATTT
1054647 AAAAAATATAATTT
1 AAAAAATATAATTT
1054661 AAAA
1 AAAA
1054665 TATTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAATATAATTT
Found at i:1054696 original size:13 final size:13
Alignment explanation
Indices: 1054633--1054697 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 13
1054623 TTTTAATTCA
*
1054633 AAAAAATATAATTT
1 AAAAAATA-AATAT
*
1054647 AAAAAATATAATTT
1 AAAAAATA-AATAT
*
1054661 AAAATATTAAATA-
1 AAAA-AATAAATAT
*
1054674 AAATAA-AAATAT
1 AAAAAATAAATAT
1054686 AAAAAATAAATA
1 AAAAAATAAATA
1054698 AATAATTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.12
12 6 0.14
13 8 0.19
14 21 0.49
15 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAAATAAATAT
Found at i:1054698 original size:19 final size:19
Alignment explanation
Indices: 1054646--1054710 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
1054636 AAATATAATT
*
1054646 TAAAAAATATAATTTAAAATA
1 TAAAAAATA-AA-TAAAAATA
* *
1054667 TTAAATA-AAATAAAAATA
1 TAAAAAATAAATAAAAATA
1054685 TAAAAAATAAATAAATAAT-
1 TAAAAAATAAATAAA-AATA
1054704 TAAAAAA
1 TAAAAAA
1054711 ATTTAAACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 12 0.32
19 16 0.43
20 4 0.11
21 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAATAAATAAAAATA
Found at i:1060706 original size:75 final size:75
Alignment explanation
Indices: 1060614--1060764 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
1060604 CCTAGTTGCT
*
1060614 TAAAACAACAATCAGACCAATGTACAGCCTTGCTGACATTTAAATTCTCTGCCATTTCATGTCGA
1 TAAAACAACAATCAGACCAATGTACAGCATTGCTGACATTTAAATTCTCTGCCATTTCATGTCGA
1060679 CCAAACATGC
66 CCAAACATGC
* *
1060689 TAAAACAACTATTAGACCAATGTACAGCATTGCTGACATTTAAATTCTCTGCCATTTCATGTCGA
1 TAAAACAACAATCAGACCAATGTACAGCATTGCTGACATTTAAATTCTCTGCCATTTCATGTCGA
1060754 CCAAACATGC
66 CCAAACATGC
1060764 T
1 T
1060765 GGTTGCCTAG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (75 bp):
TAAAACAACAATCAGACCAATGTACAGCATTGCTGACATTTAAATTCTCTGCCATTTCATGTCGA
CCAAACATGC
Found at i:1063755 original size:63 final size:63
Alignment explanation
Indices: 1063656--1063784 Score: 240
Period size: 63 Copynumber: 2.0 Consensus size: 63
1063646 CTTAAGGCTA
*
1063656 ATATTATTTATAAGAATATTTTTACATTAAATATAGTCAATAAAGATAATTTGATGATTTTTC
1 ATATTATTTATAAAAATATTTTTACATTAAATATAGTCAATAAAGATAATTTGATGATTTTTC
*
1063719 ATATTATTTATAAAAATATTTTTACATTAAATATAGTTAATAAAGATAATTTGATGATTTTTC
1 ATATTATTTATAAAAATATTTTTACATTAAATATAGTCAATAAAGATAATTTGATGATTTTTC
1063782 ATA
1 ATA
1063785 CTTTAAATAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (63 bp):
ATATTATTTATAAAAATATTTTTACATTAAATATAGTCAATAAAGATAATTTGATGATTTTTC
Found at i:1063762 original size:30 final size:30
Alignment explanation
Indices: 1063665--1063762 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
1063655 AATATTATTT
* *
1063665 ATAAGAATATTTTTACATTAAATATAGTCA
1 ATAAAAATATTTTTACATTAAATATAGTTA
* * ** ** *
1063695 ATAAAGATAATTTGATGATTTTTCATATTA-TTT
1 ATAAAAAT-ATTT--TTACATTAAATA-TAGTTA
1063728 ATAAAAATATTTTTACATTAAATATAGTTA
1 ATAAAAATATTTTTACATTAAATATAGTTA
1063758 ATAAA
1 ATAAA
1063763 GATAATTTGA
Statistics
Matches: 47, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
29 2 0.04
30 20 0.43
31 4 0.09
32 4 0.09
33 15 0.32
34 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (30 bp):
ATAAAAATATTTTTACATTAAATATAGTTA
Done.